http://www2.unil.ch/cbg/api.php?action=feedcontributions&user=Andreas&feedformat=atomComputational Biology Group - User contributions [en]2013-05-22T13:23:28ZUser contributionsMediaWiki 1.19.1http://www2.unil.ch/cbg/index.php?title=File:Expressionview.ordering.pdfFile:Expressionview.ordering.pdf2010-03-19T19:07:23Z<p>Andreas: uploaded a new version of "File:Expressionview.ordering.pdf"</p>
<hr />
<div></div>Andreashttp://www2.unil.ch/cbg/index.php?title=File:ExpressionView.tutorial.pdfFile:ExpressionView.tutorial.pdf2010-03-19T19:06:38Z<p>Andreas: </p>
<hr />
<div></div>Andreashttp://www2.unil.ch/cbg/index.php?title=ExpressionViewExpressionView2010-03-19T18:55:14Z<p>Andreas: /* Installing the stand-alone version */</p>
<hr />
<div>[[image:Expressionview.screenshot.png|Screenshot of the ExpressionView applet|500px|left]]<br />
<br style="clear: both" /><br />
<br><br />
ExpressionView is an R package that provides an interactive environment to explore biclusters identified in gene expression data. A sophisticated ordering algorithm is used to present the biclusters in a visually appealing layout. From this overview, the user can select individual biclusters and access all the biologically relevant data associated with it. The package is aimed to facilitate the collaboration between bioinformaticians and life scientists who are not familiar with the R language.<br />
<br />
= Launch and download =<br />
The ExpressionView package contains two independent parts: An ordering algorithm implemented in C++ and an Adobe Flash applet written in ActionScript and Adobe Flex. These two programs are wrapped in an R package, allowing the user to take advantage of the powerful microarray analysis tools provided by the Bioconductor project. The Flash applet itself does not require a working R environment, it can be launched in any web browser via the links provided below. If you prefer a stand-alone program, you can also download the platform independent Adobe AIR version. <br />
<br />
== Launch the ExpressionView Flash applet == <br />
* [http://www2.unil.ch/cbg/software/expressionview/flash/ExpressionView.html Launch ExpressionView]<br />
* [http://www2.unil.ch/cbg/software/expressionview/flash/ExpressionView.html?filename=../data/Expressionview.sampledata.all.small.evf Launch ExpressionView with adult T-cell acute lymphocytic leukemia (ALL) data (8 modules)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/flash/ExpressionView.html?filename=../data/Expressionview.sampledata.all.large.evf Launch ExpressionView with adult T-cell acute lymphocytic leukemia (ALL) data (108 modules)]<br />
<br />
== Download the R package (includes the Flash applet) ==<br />
* [http://www2.unil.ch/cbg/software/expressionview/r/ExpressionView_0.2.6_windows.zip Windows binary package]<br />
* [http://www2.unil.ch/cbg/software/expressionview/r/ExpressionView_0.2.6_macosx_32.tar.gz Mac OS X 32 bit binary package], [http://www2.unil.ch/cbg/software/expressionview/r/ExpressionView_0.2.6_macosx_64.tar.gz Mac OS X 64 bit binary package]<br />
* [http://www2.unil.ch/cbg/software/expressionview/r/ExpressionView_0.2.6_source.tar.gz Source package]<br />
Note that ExpressionView requires the '''[[ISA|eisa R package]]'''.<br />
<br />
== Download the stand-alone viewer (Adobe AIR) ==<br />
If you prefer a stand-alone viewer, you can download and install the Adobe AIR build [http://www2.unil.ch/cbg/software/expressionview/air/ExpressionView.air ExpressionView.air] (right-click to download file).<br><br />
To run the program, you need the AIR runtime environment which you can get from [http://get.adobe.com/air Adobe].<br><br />
ExpressionView creates files associations to .evf files, allowing you to simply double-click on such files to launch the viewer and load the data.<br />
<br />
== Download sample data ==<br />
* [http://www2.unil.ch/cbg/software/expressionview/data/Expressionview.sampledata.all.small.evf Gene expression profile of adult T-cell acute lymphocytic leukemia (ALL) with 8 modules] (right-click to download file).<br />
* [http://www2.unil.ch/cbg/software/expressionview/data/Expressionview.sampledata.all.large.evf Gene expression profile of adult T-cell acute lymphocytic leukemia (ALL) with 108 modules] (right-click to download file).<br />
<br />
= Screenshots = <br />
<gallery widths="200px" heights="109px" perrow="3"><br />
image:Expressionview.screenshot.1.png|Startup screen<br />
image:Expressionview.screenshot.2.png|Global view after loading dataset<br />
image:Expressionview.screenshot.3.png|Highlighting modules<br />
image:Expressionview.screenshot.4.png|Zoom functions<br />
image:Expressionview.screenshot.5.png|Highlighting genes (probes) and samples<br />
image:Expressionview.screenshot.6.png|GO and KEGG associations<br />
image:Expressionview.screenshot.7.png|Modules view emphasizing the underlying gene expression data<br />
image:Expressionview.screenshot.8.png|Global view without gene expression data<br />
image:Expressionview.screenshot.9.png|Experiment description<br />
</gallery><br />
<br />
= Tutorials =<br />
There are several tutorials describing how to use ExpressionView. The features of the R package are documented within the program. Just have a look at the ExpressionView help page after you have installed the package. Below, you can download the tutorial presenting the basic workflow and the description of the ordering algorithm. For the Flash applet, we have produced a few videos showing you how to use the program. <br />
<br />
== R package ==<br />
* [[Media:Expressionview.tutorial.pdf|Getting started with ExpressionView]]<br />
* [[Media:Expressionview.ordering.pdf|Ordering algorithm]]<br />
<br />
== Flash applet ==<br />
* [[Media:Expressionview.quickhelp.pdf|Quick help (pdf)]]<br />
<br />
<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.getting.started.mov Getting started (video tutorial, 6 minutes)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.tables.mov Using the tables (video tutorial, 6 minutes)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.modularview.mov Modular view (video tutorial, 4 minutes)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.view.mov Fullscreen feature (video tutorial, 1 minute)]<br />
<br />
== Installing the stand-alone version == <br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.standalone.mov Stand-alone installation (video tutorial, 2 minutes)]<br />
<br />
= Additional documentation and downloads =<br />
The Flash applet is written in ActionScript. It is open source and can be built from the command line using the Adobe Flex SDK or more conveniently with the Adobe Flex Builder IDE. For more information, visit the [http://www.adobe.com/flex Flex website].<br />
* [http://www2.unil.ch/cbg/software/expressionview/source/ExpressionView.tar.gz ExpressionView source code (for the Flash applet)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/doc ActionScript source code documentation]<br />
* [[Media:Expressionview.xmldescription.pdf|Documentation of the XML file structure]]<br />
<br />
For the Flash applet, we have implemented components that could also be used in other applications. The most important one being the LargeBitmapData class that allows one to work with BitmapData of arbitrary size. In the [http://livedocs.adobe.com/flex/3/langref/flash/display/BitmapData.html standard BitmapData class], the maximum size for a BitmapData object is 8,192 pixels in width or height, and the total number of pixels cannot exceed 16,777,216 pixels. Note that the ResizablePanel class is no longer used in ExpressionView. <br />
* [[Media:Expressionview.largebitmapdata.tar.gz|ActionScript implementation of the LargeBitmapData class (allows to use bitmaps of arbitrary dimensions)]]<br />
* [[Media:Expressionview.resizablepanel.tar.gz|ActionScript implementation of the ResizablePanel class (a panel with open, maximize, minimize, close and resize buttons)]]</div>Andreashttp://www2.unil.ch/cbg/index.php?title=ExpressionViewExpressionView2010-03-19T18:54:58Z<p>Andreas: /* Flash applet */</p>
<hr />
<div>[[image:Expressionview.screenshot.png|Screenshot of the ExpressionView applet|500px|left]]<br />
<br style="clear: both" /><br />
<br><br />
ExpressionView is an R package that provides an interactive environment to explore biclusters identified in gene expression data. A sophisticated ordering algorithm is used to present the biclusters in a visually appealing layout. From this overview, the user can select individual biclusters and access all the biologically relevant data associated with it. The package is aimed to facilitate the collaboration between bioinformaticians and life scientists who are not familiar with the R language.<br />
<br />
= Launch and download =<br />
The ExpressionView package contains two independent parts: An ordering algorithm implemented in C++ and an Adobe Flash applet written in ActionScript and Adobe Flex. These two programs are wrapped in an R package, allowing the user to take advantage of the powerful microarray analysis tools provided by the Bioconductor project. The Flash applet itself does not require a working R environment, it can be launched in any web browser via the links provided below. If you prefer a stand-alone program, you can also download the platform independent Adobe AIR version. <br />
<br />
== Launch the ExpressionView Flash applet == <br />
* [http://www2.unil.ch/cbg/software/expressionview/flash/ExpressionView.html Launch ExpressionView]<br />
* [http://www2.unil.ch/cbg/software/expressionview/flash/ExpressionView.html?filename=../data/Expressionview.sampledata.all.small.evf Launch ExpressionView with adult T-cell acute lymphocytic leukemia (ALL) data (8 modules)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/flash/ExpressionView.html?filename=../data/Expressionview.sampledata.all.large.evf Launch ExpressionView with adult T-cell acute lymphocytic leukemia (ALL) data (108 modules)]<br />
<br />
== Download the R package (includes the Flash applet) ==<br />
* [http://www2.unil.ch/cbg/software/expressionview/r/ExpressionView_0.2.6_windows.zip Windows binary package]<br />
* [http://www2.unil.ch/cbg/software/expressionview/r/ExpressionView_0.2.6_macosx_32.tar.gz Mac OS X 32 bit binary package], [http://www2.unil.ch/cbg/software/expressionview/r/ExpressionView_0.2.6_macosx_64.tar.gz Mac OS X 64 bit binary package]<br />
* [http://www2.unil.ch/cbg/software/expressionview/r/ExpressionView_0.2.6_source.tar.gz Source package]<br />
Note that ExpressionView requires the '''[[ISA|eisa R package]]'''.<br />
<br />
== Download the stand-alone viewer (Adobe AIR) ==<br />
If you prefer a stand-alone viewer, you can download and install the Adobe AIR build [http://www2.unil.ch/cbg/software/expressionview/air/ExpressionView.air ExpressionView.air] (right-click to download file).<br><br />
To run the program, you need the AIR runtime environment which you can get from [http://get.adobe.com/air Adobe].<br><br />
ExpressionView creates files associations to .evf files, allowing you to simply double-click on such files to launch the viewer and load the data.<br />
<br />
== Download sample data ==<br />
* [http://www2.unil.ch/cbg/software/expressionview/data/Expressionview.sampledata.all.small.evf Gene expression profile of adult T-cell acute lymphocytic leukemia (ALL) with 8 modules] (right-click to download file).<br />
* [http://www2.unil.ch/cbg/software/expressionview/data/Expressionview.sampledata.all.large.evf Gene expression profile of adult T-cell acute lymphocytic leukemia (ALL) with 108 modules] (right-click to download file).<br />
<br />
= Screenshots = <br />
<gallery widths="200px" heights="109px" perrow="3"><br />
image:Expressionview.screenshot.1.png|Startup screen<br />
image:Expressionview.screenshot.2.png|Global view after loading dataset<br />
image:Expressionview.screenshot.3.png|Highlighting modules<br />
image:Expressionview.screenshot.4.png|Zoom functions<br />
image:Expressionview.screenshot.5.png|Highlighting genes (probes) and samples<br />
image:Expressionview.screenshot.6.png|GO and KEGG associations<br />
image:Expressionview.screenshot.7.png|Modules view emphasizing the underlying gene expression data<br />
image:Expressionview.screenshot.8.png|Global view without gene expression data<br />
image:Expressionview.screenshot.9.png|Experiment description<br />
</gallery><br />
<br />
= Tutorials =<br />
There are several tutorials describing how to use ExpressionView. The features of the R package are documented within the program. Just have a look at the ExpressionView help page after you have installed the package. Below, you can download the tutorial presenting the basic workflow and the description of the ordering algorithm. For the Flash applet, we have produced a few videos showing you how to use the program. <br />
<br />
== R package ==<br />
* [[Media:Expressionview.tutorial.pdf|Getting started with ExpressionView]]<br />
* [[Media:Expressionview.ordering.pdf|Ordering algorithm]]<br />
<br />
== Flash applet ==<br />
* [[Media:Expressionview.quickhelp.pdf|Quick help (pdf)]]<br />
<br />
<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.getting.started.mov Getting started (video tutorial, 6 minutes)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.tables.mov Using the tables (video tutorial, 6 minutes)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.modularview.mov Modular view (video tutorial, 4 minutes)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.view.mov Fullscreen feature (video tutorial, 1 minute)]<br />
<br />
== Installing the stand-alone version == <br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videoutorial.standalone.mov Stand-alone installation (video tutorial, 2 minutes)]<br />
<br />
= Additional documentation and downloads =<br />
The Flash applet is written in ActionScript. It is open source and can be built from the command line using the Adobe Flex SDK or more conveniently with the Adobe Flex Builder IDE. For more information, visit the [http://www.adobe.com/flex Flex website].<br />
* [http://www2.unil.ch/cbg/software/expressionview/source/ExpressionView.tar.gz ExpressionView source code (for the Flash applet)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/doc ActionScript source code documentation]<br />
* [[Media:Expressionview.xmldescription.pdf|Documentation of the XML file structure]]<br />
<br />
For the Flash applet, we have implemented components that could also be used in other applications. The most important one being the LargeBitmapData class that allows one to work with BitmapData of arbitrary size. In the [http://livedocs.adobe.com/flex/3/langref/flash/display/BitmapData.html standard BitmapData class], the maximum size for a BitmapData object is 8,192 pixels in width or height, and the total number of pixels cannot exceed 16,777,216 pixels. Note that the ResizablePanel class is no longer used in ExpressionView. <br />
* [[Media:Expressionview.largebitmapdata.tar.gz|ActionScript implementation of the LargeBitmapData class (allows to use bitmaps of arbitrary dimensions)]]<br />
* [[Media:Expressionview.resizablepanel.tar.gz|ActionScript implementation of the ResizablePanel class (a panel with open, maximize, minimize, close and resize buttons)]]</div>Andreashttp://www2.unil.ch/cbg/index.php?title=ExpressionViewExpressionView2010-03-19T18:53:44Z<p>Andreas: /* Download the R package (includes the Flash applet) */</p>
<hr />
<div>[[image:Expressionview.screenshot.png|Screenshot of the ExpressionView applet|500px|left]]<br />
<br style="clear: both" /><br />
<br><br />
ExpressionView is an R package that provides an interactive environment to explore biclusters identified in gene expression data. A sophisticated ordering algorithm is used to present the biclusters in a visually appealing layout. From this overview, the user can select individual biclusters and access all the biologically relevant data associated with it. The package is aimed to facilitate the collaboration between bioinformaticians and life scientists who are not familiar with the R language.<br />
<br />
= Launch and download =<br />
The ExpressionView package contains two independent parts: An ordering algorithm implemented in C++ and an Adobe Flash applet written in ActionScript and Adobe Flex. These two programs are wrapped in an R package, allowing the user to take advantage of the powerful microarray analysis tools provided by the Bioconductor project. The Flash applet itself does not require a working R environment, it can be launched in any web browser via the links provided below. If you prefer a stand-alone program, you can also download the platform independent Adobe AIR version. <br />
<br />
== Launch the ExpressionView Flash applet == <br />
* [http://www2.unil.ch/cbg/software/expressionview/flash/ExpressionView.html Launch ExpressionView]<br />
* [http://www2.unil.ch/cbg/software/expressionview/flash/ExpressionView.html?filename=../data/Expressionview.sampledata.all.small.evf Launch ExpressionView with adult T-cell acute lymphocytic leukemia (ALL) data (8 modules)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/flash/ExpressionView.html?filename=../data/Expressionview.sampledata.all.large.evf Launch ExpressionView with adult T-cell acute lymphocytic leukemia (ALL) data (108 modules)]<br />
<br />
== Download the R package (includes the Flash applet) ==<br />
* [http://www2.unil.ch/cbg/software/expressionview/r/ExpressionView_0.2.6_windows.zip Windows binary package]<br />
* [http://www2.unil.ch/cbg/software/expressionview/r/ExpressionView_0.2.6_macosx_32.tar.gz Mac OS X 32 bit binary package], [http://www2.unil.ch/cbg/software/expressionview/r/ExpressionView_0.2.6_macosx_64.tar.gz Mac OS X 64 bit binary package]<br />
* [http://www2.unil.ch/cbg/software/expressionview/r/ExpressionView_0.2.6_source.tar.gz Source package]<br />
Note that ExpressionView requires the '''[[ISA|eisa R package]]'''.<br />
<br />
== Download the stand-alone viewer (Adobe AIR) ==<br />
If you prefer a stand-alone viewer, you can download and install the Adobe AIR build [http://www2.unil.ch/cbg/software/expressionview/air/ExpressionView.air ExpressionView.air] (right-click to download file).<br><br />
To run the program, you need the AIR runtime environment which you can get from [http://get.adobe.com/air Adobe].<br><br />
ExpressionView creates files associations to .evf files, allowing you to simply double-click on such files to launch the viewer and load the data.<br />
<br />
== Download sample data ==<br />
* [http://www2.unil.ch/cbg/software/expressionview/data/Expressionview.sampledata.all.small.evf Gene expression profile of adult T-cell acute lymphocytic leukemia (ALL) with 8 modules] (right-click to download file).<br />
* [http://www2.unil.ch/cbg/software/expressionview/data/Expressionview.sampledata.all.large.evf Gene expression profile of adult T-cell acute lymphocytic leukemia (ALL) with 108 modules] (right-click to download file).<br />
<br />
= Screenshots = <br />
<gallery widths="200px" heights="109px" perrow="3"><br />
image:Expressionview.screenshot.1.png|Startup screen<br />
image:Expressionview.screenshot.2.png|Global view after loading dataset<br />
image:Expressionview.screenshot.3.png|Highlighting modules<br />
image:Expressionview.screenshot.4.png|Zoom functions<br />
image:Expressionview.screenshot.5.png|Highlighting genes (probes) and samples<br />
image:Expressionview.screenshot.6.png|GO and KEGG associations<br />
image:Expressionview.screenshot.7.png|Modules view emphasizing the underlying gene expression data<br />
image:Expressionview.screenshot.8.png|Global view without gene expression data<br />
image:Expressionview.screenshot.9.png|Experiment description<br />
</gallery><br />
<br />
= Tutorials =<br />
There are several tutorials describing how to use ExpressionView. The features of the R package are documented within the program. Just have a look at the ExpressionView help page after you have installed the package. Below, you can download the tutorial presenting the basic workflow and the description of the ordering algorithm. For the Flash applet, we have produced a few videos showing you how to use the program. <br />
<br />
== R package ==<br />
* [[Media:Expressionview.tutorial.pdf|Getting started with ExpressionView]]<br />
* [[Media:Expressionview.ordering.pdf|Ordering algorithm]]<br />
<br />
== Flash applet ==<br />
* [[Media:Expressionview.quickhelp.pdf|Quick help (pdf)]]<br />
<br />
<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.getting.started.mov Getting started (video tutorial, 6 minutes)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.tables.mov Using the tables (video tutorial, 6 minutes)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.modularview.mov Modular view (video tutorial, 4 minutes)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorials.view.mov Fullscreen feature (video tutorial, 1 minute)]<br />
<br />
== Installing the stand-alone version == <br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videoutorial.standalone.mov Stand-alone installation (video tutorial, 2 minutes)]<br />
<br />
= Additional documentation and downloads =<br />
The Flash applet is written in ActionScript. It is open source and can be built from the command line using the Adobe Flex SDK or more conveniently with the Adobe Flex Builder IDE. For more information, visit the [http://www.adobe.com/flex Flex website].<br />
* [http://www2.unil.ch/cbg/software/expressionview/source/ExpressionView.tar.gz ExpressionView source code (for the Flash applet)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/doc ActionScript source code documentation]<br />
* [[Media:Expressionview.xmldescription.pdf|Documentation of the XML file structure]]<br />
<br />
For the Flash applet, we have implemented components that could also be used in other applications. The most important one being the LargeBitmapData class that allows one to work with BitmapData of arbitrary size. In the [http://livedocs.adobe.com/flex/3/langref/flash/display/BitmapData.html standard BitmapData class], the maximum size for a BitmapData object is 8,192 pixels in width or height, and the total number of pixels cannot exceed 16,777,216 pixels. Note that the ResizablePanel class is no longer used in ExpressionView. <br />
* [[Media:Expressionview.largebitmapdata.tar.gz|ActionScript implementation of the LargeBitmapData class (allows to use bitmaps of arbitrary dimensions)]]<br />
* [[Media:Expressionview.resizablepanel.tar.gz|ActionScript implementation of the ResizablePanel class (a panel with open, maximize, minimize, close and resize buttons)]]</div>Andreashttp://www2.unil.ch/cbg/index.php?title=ExpressionViewExpressionView2009-12-11T07:30:36Z<p>Andreas: /* Download the R package (includes the Flash applet) */</p>
<hr />
<div>[[image:Expressionview.screenshot.png|Screenshot of the ExpressionView applet|500px|left]]<br />
<br style="clear: both" /><br />
<br><br />
ExpressionView is an R package that provides an interactive environment to explore biclusters identified in gene expression data. A sophisticated ordering algorithm is used to present the biclusters in a visually appealing layout. From this overview, the user can select individual biclusters and access all the biologically relevant data associated with it. The package is aimed to facilitate the collaboration between bioinformaticians and life scientists who are not familiar with the R language.<br />
<br />
= Launch and download =<br />
The ExpressionView package contains two independent parts: An ordering algorithm implemented in C++ and an Adobe Flash applet written in ActionScript and Adobe Flex. These two programs are wrapped in an R package, allowing the user to take advantage of the powerful microarray analysis tools provided by the Bioconductor project. The Flash applet itself does not require a working R environment, it can be launched in any web browser via the links provided below. If you prefer a stand-alone program, you can also download the platform independent Adobe AIR version. <br />
<br />
== Launch the ExpressionView Flash applet == <br />
* [http://www2.unil.ch/cbg/software/expressionview/flash/ExpressionView.html Launch ExpressionView]<br />
* [http://www2.unil.ch/cbg/software/expressionview/flash/ExpressionView.html?filename=../data/Expressionview.sampledata.all.small.evf Launch ExpressionView with adult T-cell acute lymphocytic leukemia (ALL) data (8 modules)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/flash/ExpressionView.html?filename=../data/Expressionview.sampledata.all.large.evf Launch ExpressionView with adult T-cell acute lymphocytic leukemia (ALL) data (108 modules)]<br />
<br />
== Download the R package (includes the Flash applet) ==<br />
* [http://www2.unil.ch/cbg/software/expressionview/r/ExpressionView_0.2.1.zip Windows binary package]<br />
* [http://www2.unil.ch/cbg/software/expressionview/r/ExpressionView_0.2.1_macosx_32.tar.gz Mac OS X 32 bit binary package], [http://www2.unil.ch/cbg/software/expressionview/r/ExpressionView_0.2.1_macosx_64.tar.gz Mac OS X 64 bit binary package]<br />
* [http://www2.unil.ch/cbg/software/expressionview/r/ExpressionView_0.2.1_source.tar.gz Source package]<br />
Note that ExpressionView requires the '''[[ISA|ISA package]]'''.<br />
<br />
== Download the stand-alone viewer (Adobe AIR) ==<br />
If you prefer a stand-alone viewer, you can download and install the Adobe AIR build [http://www2.unil.ch/cbg/software/expressionview/air/ExpressionView.air ExpressionView.air] (right-click to download file).<br><br />
To run the program, you need the AIR runtime environment which you can get from [http://get.adobe.com/air Adobe].<br><br />
ExpressionView creates files associations to .evf files, allowing you to simply double-click on such files to launch the viewer and load the data.<br />
<br />
== Download sample data ==<br />
* [http://www2.unil.ch/cbg/software/expressionview/data/Expressionview.sampledata.all.small.evf Gene expression profile of adult T-cell acute lymphocytic leukemia (ALL) with 8 modules] (right-click to download file).<br />
* [http://www2.unil.ch/cbg/software/expressionview/data/Expressionview.sampledata.all.large.evf Gene expression profile of adult T-cell acute lymphocytic leukemia (ALL) with 108 modules] (right-click to download file).<br />
<br />
= Screenshots = <br />
<gallery widths="200px" heights="109px" perrow="3"><br />
image:Expressionview.screenshot.1.png|Startup screen<br />
image:Expressionview.screenshot.2.png|Global view after loading dataset<br />
image:Expressionview.screenshot.3.png|Highlighting modules<br />
image:Expressionview.screenshot.4.png|Zoom functions<br />
image:Expressionview.screenshot.5.png|Highlighting genes (probes) and samples<br />
image:Expressionview.screenshot.6.png|GO and KEGG associations<br />
image:Expressionview.screenshot.7.png|Modules view emphasizing the underlying gene expression data<br />
image:Expressionview.screenshot.8.png|Global view without gene expression data<br />
image:Expressionview.screenshot.9.png|Experiment description<br />
</gallery><br />
<br />
= Tutorials =<br />
There are several tutorials describing how to use ExpressionView. The features of the R package are documented within the program. Just have a look at the ExpressionView help page after you have installed the package. Below, you can download the tutorial presenting the basic workflow and the description of the ordering algorithm. For the Flash applet, we have produced a few videos showing you how to use the program. <br />
<br />
== R package ==<br />
* [[Media:Expressionview.tutorial.pdf|Getting started with ExpressionView]]<br />
* [[Media:Expressionview.ordering.pdf|Ordering algorithm]]<br />
<br />
== Flash applet ==<br />
* [[Media:Expressionview.quickhelp.pdf|Quick help (pdf)]]<br />
<br />
<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.getting.started.mov Getting started (video tutorial, 6 minutes)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.tables.mov Using the tables (video tutorial, 6 minutes)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.modularview.mov Modular view (video tutoria, 4 minutesl)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorials.view.mov Fullscreen feature (video tutorial, 1 minute)]<br />
<br />
== Installing the stand-alone version == <br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videoutorial.standalone.mov Stand-alone installation (video tutorial, 2 minutes)]<br />
<br />
= Additional documentation and downloads =<br />
The Flash applet is written in ActionScript. It is open source and can be built from the command line using the Adobe Flex SDK or more conveniently with the Adobe Flex Builder IDE. For more information, visit the [http://www.adobe.com/flex Flex website].<br />
* [http://www2.unil.ch/cbg/software/expressionview/source/ExpressionView.tar.gz ExpressionView source code (for the Flash applet)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/doc ActionScript source code documentation]<br />
* [[Media:Expressionview.xmldescription.pdf|Documentation of the XML file structure]]<br />
<br />
For the Flash applet, we have implemented components that could also be used in other applications. The most important one being the LargeBitmapData class that allows one to work with BitmapData of arbitrary size. In the [http://livedocs.adobe.com/flex/3/langref/flash/display/BitmapData.html standard BitmapData class], the maximum size for a BitmapData object is 8,192 pixels in width or height, and the total number of pixels cannot exceed 16,777,216 pixels. Note that the ResizablePanel class is no longer used in ExpressionView. <br />
* [[Media:Expressionview.largebitmapdata.tar.gz|ActionScript implementation of the LargeBitmapData class (allows to use bitmaps of arbitrary dimensions)]]<br />
* [[Media:Expressionview.resizablepanel.tar.gz|ActionScript implementation of the ResizablePanel class (a panel with open, maximize, minimize, close and resize buttons)]]</div>Andreashttp://www2.unil.ch/cbg/index.php?title=ExpressionViewExpressionView2009-12-04T09:16:51Z<p>Andreas: /* Installing the stand-alone version */</p>
<hr />
<div>[[image:Expressionview.screenshot.png|Screenshot of the ExpressionView applet|500px|left]]<br />
<br style="clear: both" /><br />
<br><br />
ExpressionView is an R package that provides an interactive environment to explore biclusters identified in gene expression data. A sophisticated ordering algorithm is used to present the biclusters in a visually appealing layout. From this overview, the user can select individual biclusters and access all the biologically relevant data associated with it. The package is aimed to facilitate the collaboration between bioinformaticians and life scientists who are not familiar with the R language.<br />
<br />
= Launch and download =<br />
The ExpressionView package contains two independent parts: An ordering algorithm implemented in C++ and an Adobe Flash applet written in ActionScript and Adobe Flex. These two programs are wrapped in an R package, allowing the user to take advantage of the powerful microarray analysis tools provided by the Bioconductor project. The Flash applet itself does not require a working R environment, it can be launched in any web browser via the links provided below. If you prefer a stand-alone program, you can also download the platform independent Adobe AIR version. <br />
<br />
== Launch the ExpressionView Flash applet == <br />
* [http://www2.unil.ch/cbg/software/expressionview/flash/ExpressionView.html Launch ExpressionView]<br />
* [http://www2.unil.ch/cbg/software/expressionview/flash/ExpressionView.html?filename=../data/Expressionview.sampledata.all.small.evf Launch ExpressionView with adult T-cell acute lymphocytic leukemia (ALL) data (8 modules)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/flash/ExpressionView.html?filename=../data/Expressionview.sampledata.all.large.evf Launch ExpressionView with adult T-cell acute lymphocytic leukemia (ALL) data (108 modules)]<br />
<br />
== Download the R package (includes the Flash applet) ==<br />
* [http://www2.unil.ch/cbg/software/expressionview/r/ExpressionView_0.2.1_windows.zip Windows binary package]<br />
* [http://www2.unil.ch/cbg/software/expressionview/r/ExpressionView_0.2.1_macosx_32.tar.gz Mac OS X 32 bit binary package], [http://www2.unil.ch/cbg/software/expressionview/r/ExpressionView_0.2.1_macosx_64.tar.gz Mac OS X 64 bit binary package]<br />
* [http://www2.unil.ch/cbg/software/expressionview/r/ExpressionView_0.2.1_source.tar.gz Source package]<br />
Note that ExpressionView requires the '''[[ISA|ISA package]]'''.<br />
<br />
== Download the stand-alone viewer (Adobe AIR) ==<br />
If you prefer a stand-alone viewer, you can download and install the Adobe AIR build [http://www2.unil.ch/cbg/software/expressionview/air/ExpressionView.air ExpressionView.air] (right-click to download file).<br><br />
To run the program, you need the AIR runtime environment which you can get from [http://get.adobe.com/air Adobe].<br><br />
ExpressionView creates files associations to .evf files, allowing you to simply double-click on such files to launch the viewer and load the data.<br />
<br />
== Download sample data ==<br />
* [http://www2.unil.ch/cbg/software/expressionview/data/Expressionview.sampledata.all.small.evf Gene expression profile of adult T-cell acute lymphocytic leukemia (ALL) with 8 modules] (right-click to download file).<br />
* [http://www2.unil.ch/cbg/software/expressionview/data/Expressionview.sampledata.all.large.evf Gene expression profile of adult T-cell acute lymphocytic leukemia (ALL) with 108 modules] (right-click to download file).<br />
<br />
= Screenshots = <br />
<gallery widths="200px" heights="109px" perrow="3"><br />
image:Expressionview.screenshot.1.png|Startup screen<br />
image:Expressionview.screenshot.2.png|Global view after loading dataset<br />
image:Expressionview.screenshot.3.png|Highlighting modules<br />
image:Expressionview.screenshot.4.png|Zoom functions<br />
image:Expressionview.screenshot.5.png|Highlighting genes (probes) and samples<br />
image:Expressionview.screenshot.6.png|GO and KEGG associations<br />
image:Expressionview.screenshot.7.png|Modules view emphasizing the underlying gene expression data<br />
image:Expressionview.screenshot.8.png|Global view without gene expression data<br />
image:Expressionview.screenshot.9.png|Experiment description<br />
</gallery><br />
<br />
= Tutorials =<br />
There are several tutorials describing how to use ExpressionView. The features of the R package are documented within the program. Just have a look at the ExpressionView help page after you have installed the package. Below, you can download the tutorial presenting the basic workflow and the description of the ordering algorithm. For the Flash applet, we have produced a few videos showing you how to use the program. <br />
<br />
== R package ==<br />
* [[Media:Expressionview.tutorial.pdf|Getting started with ExpressionView]]<br />
* [[Media:Expressionview.ordering.pdf|Ordering algorithm]]<br />
<br />
== Flash applet ==<br />
* [[Media:Expressionview.quickhelp.pdf|Quick help (pdf)]]<br />
<br />
<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.getting.started.mov Getting started (video tutorial, 6 minutes)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.tables.mov Using the tables (video tutorial, 6 minutes)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.modularview.mov Modular view (video tutoria, 4 minutesl)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorials.view.mov Fullscreen feature (video tutorial, 1 minute)]<br />
<br />
== Installing the stand-alone version == <br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videoutorial.standalone.mov Stand-alone installation (video tutorial, 2 minutes)]<br />
<br />
= Additional documentation and downloads =<br />
The Flash applet is written in ActionScript. It is open source and can be built from the command line using the Adobe Flex SDK or more conveniently with the Adobe Flex Builder IDE. For more information, visit the [http://www.adobe.com/flex Flex website].<br />
* [http://www2.unil.ch/cbg/software/expressionview/source/ExpressionView.tar.gz ExpressionView source code (for the Flash applet)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/doc ActionScript source code documentation]<br />
* [[Media:Expressionview.xmldescription.pdf|Documentation of the XML file structure]]<br />
<br />
For the Flash applet, we have implemented components that could also be used in other applications. The most important one being the LargeBitmapData class that allows one to work with BitmapData of arbitrary size. In the [http://livedocs.adobe.com/flex/3/langref/flash/display/BitmapData.html standard BitmapData class], the maximum size for a BitmapData object is 8,192 pixels in width or height, and the total number of pixels cannot exceed 16,777,216 pixels. Note that the ResizablePanel class is no longer used in ExpressionView. <br />
* [[Media:Expressionview.largebitmapdata.tar.gz|ActionScript implementation of the LargeBitmapData class (allows to use bitmaps of arbitrary dimensions)]]<br />
* [[Media:Expressionview.resizablepanel.tar.gz|ActionScript implementation of the ResizablePanel class (a panel with open, maximize, minimize, close and resize buttons)]]</div>Andreashttp://www2.unil.ch/cbg/index.php?title=ExpressionViewExpressionView2009-12-04T09:16:15Z<p>Andreas: /* Flash applet */</p>
<hr />
<div>[[image:Expressionview.screenshot.png|Screenshot of the ExpressionView applet|500px|left]]<br />
<br style="clear: both" /><br />
<br><br />
ExpressionView is an R package that provides an interactive environment to explore biclusters identified in gene expression data. A sophisticated ordering algorithm is used to present the biclusters in a visually appealing layout. From this overview, the user can select individual biclusters and access all the biologically relevant data associated with it. The package is aimed to facilitate the collaboration between bioinformaticians and life scientists who are not familiar with the R language.<br />
<br />
= Launch and download =<br />
The ExpressionView package contains two independent parts: An ordering algorithm implemented in C++ and an Adobe Flash applet written in ActionScript and Adobe Flex. These two programs are wrapped in an R package, allowing the user to take advantage of the powerful microarray analysis tools provided by the Bioconductor project. The Flash applet itself does not require a working R environment, it can be launched in any web browser via the links provided below. If you prefer a stand-alone program, you can also download the platform independent Adobe AIR version. <br />
<br />
== Launch the ExpressionView Flash applet == <br />
* [http://www2.unil.ch/cbg/software/expressionview/flash/ExpressionView.html Launch ExpressionView]<br />
* [http://www2.unil.ch/cbg/software/expressionview/flash/ExpressionView.html?filename=../data/Expressionview.sampledata.all.small.evf Launch ExpressionView with adult T-cell acute lymphocytic leukemia (ALL) data (8 modules)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/flash/ExpressionView.html?filename=../data/Expressionview.sampledata.all.large.evf Launch ExpressionView with adult T-cell acute lymphocytic leukemia (ALL) data (108 modules)]<br />
<br />
== Download the R package (includes the Flash applet) ==<br />
* [http://www2.unil.ch/cbg/software/expressionview/r/ExpressionView_0.2.1_windows.zip Windows binary package]<br />
* [http://www2.unil.ch/cbg/software/expressionview/r/ExpressionView_0.2.1_macosx_32.tar.gz Mac OS X 32 bit binary package], [http://www2.unil.ch/cbg/software/expressionview/r/ExpressionView_0.2.1_macosx_64.tar.gz Mac OS X 64 bit binary package]<br />
* [http://www2.unil.ch/cbg/software/expressionview/r/ExpressionView_0.2.1_source.tar.gz Source package]<br />
Note that ExpressionView requires the '''[[ISA|ISA package]]'''.<br />
<br />
== Download the stand-alone viewer (Adobe AIR) ==<br />
If you prefer a stand-alone viewer, you can download and install the Adobe AIR build [http://www2.unil.ch/cbg/software/expressionview/air/ExpressionView.air ExpressionView.air] (right-click to download file).<br><br />
To run the program, you need the AIR runtime environment which you can get from [http://get.adobe.com/air Adobe].<br><br />
ExpressionView creates files associations to .evf files, allowing you to simply double-click on such files to launch the viewer and load the data.<br />
<br />
== Download sample data ==<br />
* [http://www2.unil.ch/cbg/software/expressionview/data/Expressionview.sampledata.all.small.evf Gene expression profile of adult T-cell acute lymphocytic leukemia (ALL) with 8 modules] (right-click to download file).<br />
* [http://www2.unil.ch/cbg/software/expressionview/data/Expressionview.sampledata.all.large.evf Gene expression profile of adult T-cell acute lymphocytic leukemia (ALL) with 108 modules] (right-click to download file).<br />
<br />
= Screenshots = <br />
<gallery widths="200px" heights="109px" perrow="3"><br />
image:Expressionview.screenshot.1.png|Startup screen<br />
image:Expressionview.screenshot.2.png|Global view after loading dataset<br />
image:Expressionview.screenshot.3.png|Highlighting modules<br />
image:Expressionview.screenshot.4.png|Zoom functions<br />
image:Expressionview.screenshot.5.png|Highlighting genes (probes) and samples<br />
image:Expressionview.screenshot.6.png|GO and KEGG associations<br />
image:Expressionview.screenshot.7.png|Modules view emphasizing the underlying gene expression data<br />
image:Expressionview.screenshot.8.png|Global view without gene expression data<br />
image:Expressionview.screenshot.9.png|Experiment description<br />
</gallery><br />
<br />
= Tutorials =<br />
There are several tutorials describing how to use ExpressionView. The features of the R package are documented within the program. Just have a look at the ExpressionView help page after you have installed the package. Below, you can download the tutorial presenting the basic workflow and the description of the ordering algorithm. For the Flash applet, we have produced a few videos showing you how to use the program. <br />
<br />
== R package ==<br />
* [[Media:Expressionview.tutorial.pdf|Getting started with ExpressionView]]<br />
* [[Media:Expressionview.ordering.pdf|Ordering algorithm]]<br />
<br />
== Flash applet ==<br />
* [[Media:Expressionview.quickhelp.pdf|Quick help (pdf)]]<br />
<br />
<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.getting.started.mov Getting started (video tutorial, 6 minutes)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.tables.mov Using the tables (video tutorial, 6 minutes)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.modularview.mov Modular view (video tutoria, 4 minutesl)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorials.view.mov Fullscreen feature (video tutorial, 1 minute)]<br />
<br />
== Installing the stand-alone version == <br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.standalone.mov Stand-alone installation (video tutorial, 2 minutes)]<br />
<br />
= Additional documentation and downloads =<br />
The Flash applet is written in ActionScript. It is open source and can be built from the command line using the Adobe Flex SDK or more conveniently with the Adobe Flex Builder IDE. For more information, visit the [http://www.adobe.com/flex Flex website].<br />
* [http://www2.unil.ch/cbg/software/expressionview/source/ExpressionView.tar.gz ExpressionView source code (for the Flash applet)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/doc ActionScript source code documentation]<br />
* [[Media:Expressionview.xmldescription.pdf|Documentation of the XML file structure]]<br />
<br />
For the Flash applet, we have implemented components that could also be used in other applications. The most important one being the LargeBitmapData class that allows one to work with BitmapData of arbitrary size. In the [http://livedocs.adobe.com/flex/3/langref/flash/display/BitmapData.html standard BitmapData class], the maximum size for a BitmapData object is 8,192 pixels in width or height, and the total number of pixels cannot exceed 16,777,216 pixels. Note that the ResizablePanel class is no longer used in ExpressionView. <br />
* [[Media:Expressionview.largebitmapdata.tar.gz|ActionScript implementation of the LargeBitmapData class (allows to use bitmaps of arbitrary dimensions)]]<br />
* [[Media:Expressionview.resizablepanel.tar.gz|ActionScript implementation of the ResizablePanel class (a panel with open, maximize, minimize, close and resize buttons)]]</div>Andreashttp://www2.unil.ch/cbg/index.php?title=ExpressionViewExpressionView2009-12-04T09:14:11Z<p>Andreas: /* Download sample data */</p>
<hr />
<div>[[image:Expressionview.screenshot.png|Screenshot of the ExpressionView applet|500px|left]]<br />
<br style="clear: both" /><br />
<br><br />
ExpressionView is an R package that provides an interactive environment to explore biclusters identified in gene expression data. A sophisticated ordering algorithm is used to present the biclusters in a visually appealing layout. From this overview, the user can select individual biclusters and access all the biologically relevant data associated with it. The package is aimed to facilitate the collaboration between bioinformaticians and life scientists who are not familiar with the R language.<br />
<br />
= Launch and download =<br />
The ExpressionView package contains two independent parts: An ordering algorithm implemented in C++ and an Adobe Flash applet written in ActionScript and Adobe Flex. These two programs are wrapped in an R package, allowing the user to take advantage of the powerful microarray analysis tools provided by the Bioconductor project. The Flash applet itself does not require a working R environment, it can be launched in any web browser via the links provided below. If you prefer a stand-alone program, you can also download the platform independent Adobe AIR version. <br />
<br />
== Launch the ExpressionView Flash applet == <br />
* [http://www2.unil.ch/cbg/software/expressionview/flash/ExpressionView.html Launch ExpressionView]<br />
* [http://www2.unil.ch/cbg/software/expressionview/flash/ExpressionView.html?filename=../data/Expressionview.sampledata.all.small.evf Launch ExpressionView with adult T-cell acute lymphocytic leukemia (ALL) data (8 modules)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/flash/ExpressionView.html?filename=../data/Expressionview.sampledata.all.large.evf Launch ExpressionView with adult T-cell acute lymphocytic leukemia (ALL) data (108 modules)]<br />
<br />
== Download the R package (includes the Flash applet) ==<br />
* [http://www2.unil.ch/cbg/software/expressionview/r/ExpressionView_0.2.1_windows.zip Windows binary package]<br />
* [http://www2.unil.ch/cbg/software/expressionview/r/ExpressionView_0.2.1_macosx_32.tar.gz Mac OS X 32 bit binary package], [http://www2.unil.ch/cbg/software/expressionview/r/ExpressionView_0.2.1_macosx_64.tar.gz Mac OS X 64 bit binary package]<br />
* [http://www2.unil.ch/cbg/software/expressionview/r/ExpressionView_0.2.1_source.tar.gz Source package]<br />
Note that ExpressionView requires the '''[[ISA|ISA package]]'''.<br />
<br />
== Download the stand-alone viewer (Adobe AIR) ==<br />
If you prefer a stand-alone viewer, you can download and install the Adobe AIR build [http://www2.unil.ch/cbg/software/expressionview/air/ExpressionView.air ExpressionView.air] (right-click to download file).<br><br />
To run the program, you need the AIR runtime environment which you can get from [http://get.adobe.com/air Adobe].<br><br />
ExpressionView creates files associations to .evf files, allowing you to simply double-click on such files to launch the viewer and load the data.<br />
<br />
== Download sample data ==<br />
* [http://www2.unil.ch/cbg/software/expressionview/data/Expressionview.sampledata.all.small.evf Gene expression profile of adult T-cell acute lymphocytic leukemia (ALL) with 8 modules] (right-click to download file).<br />
* [http://www2.unil.ch/cbg/software/expressionview/data/Expressionview.sampledata.all.large.evf Gene expression profile of adult T-cell acute lymphocytic leukemia (ALL) with 108 modules] (right-click to download file).<br />
<br />
= Screenshots = <br />
<gallery widths="200px" heights="109px" perrow="3"><br />
image:Expressionview.screenshot.1.png|Startup screen<br />
image:Expressionview.screenshot.2.png|Global view after loading dataset<br />
image:Expressionview.screenshot.3.png|Highlighting modules<br />
image:Expressionview.screenshot.4.png|Zoom functions<br />
image:Expressionview.screenshot.5.png|Highlighting genes (probes) and samples<br />
image:Expressionview.screenshot.6.png|GO and KEGG associations<br />
image:Expressionview.screenshot.7.png|Modules view emphasizing the underlying gene expression data<br />
image:Expressionview.screenshot.8.png|Global view without gene expression data<br />
image:Expressionview.screenshot.9.png|Experiment description<br />
</gallery><br />
<br />
= Tutorials =<br />
There are several tutorials describing how to use ExpressionView. The features of the R package are documented within the program. Just have a look at the ExpressionView help page after you have installed the package. Below, you can download the tutorial presenting the basic workflow and the description of the ordering algorithm. For the Flash applet, we have produced a few videos showing you how to use the program. <br />
<br />
== R package ==<br />
* [[Media:Expressionview.tutorial.pdf|Getting started with ExpressionView]]<br />
* [[Media:Expressionview.ordering.pdf|Ordering algorithm]]<br />
<br />
== Flash applet ==<br />
* [[Media:Expressionview.quickhelp.pdf|Quick help (pdf)]]<br />
<br />
<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.getting.started.mov Getting started (video tutorial, 6 minutes)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.tables.mov Using the tables (video tutorial, 6 minutes)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.modularview.mov Modular view (video tutoria, 4 minutesl)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.view.mov Fullscreen feature (video tutorial, 1 minute)]<br />
<br />
== Installing the stand-alone version == <br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.standalone.mov Stand-alone installation (video tutorial, 2 minutes)]<br />
<br />
= Additional documentation and downloads =<br />
The Flash applet is written in ActionScript. It is open source and can be built from the command line using the Adobe Flex SDK or more conveniently with the Adobe Flex Builder IDE. For more information, visit the [http://www.adobe.com/flex Flex website].<br />
* [http://www2.unil.ch/cbg/software/expressionview/source/ExpressionView.tar.gz ExpressionView source code (for the Flash applet)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/doc ActionScript source code documentation]<br />
* [[Media:Expressionview.xmldescription.pdf|Documentation of the XML file structure]]<br />
<br />
For the Flash applet, we have implemented components that could also be used in other applications. The most important one being the LargeBitmapData class that allows one to work with BitmapData of arbitrary size. In the [http://livedocs.adobe.com/flex/3/langref/flash/display/BitmapData.html standard BitmapData class], the maximum size for a BitmapData object is 8,192 pixels in width or height, and the total number of pixels cannot exceed 16,777,216 pixels. Note that the ResizablePanel class is no longer used in ExpressionView. <br />
* [[Media:Expressionview.largebitmapdata.tar.gz|ActionScript implementation of the LargeBitmapData class (allows to use bitmaps of arbitrary dimensions)]]<br />
* [[Media:Expressionview.resizablepanel.tar.gz|ActionScript implementation of the ResizablePanel class (a panel with open, maximize, minimize, close and resize buttons)]]</div>Andreashttp://www2.unil.ch/cbg/index.php?title=ExpressionViewExpressionView2009-12-03T07:58:29Z<p>Andreas: </p>
<hr />
<div>[[image:Expressionview.screenshot.png|Screenshot of the ExpressionView applet|500px|left]]<br />
<br style="clear: both" /><br />
<br><br />
ExpressionView is an R package that provides an interactive environment to explore biclusters identified in gene expression data. A sophisticated ordering algorithm is used to present the biclusters in a visually appealing layout. From this overview, the user can select individual biclusters and access all the biologically relevant data associated with it. The package is aimed to facilitate the collaboration between bioinformaticians and life scientists who are not familiar with the R language.<br />
<br />
= Launch and download =<br />
The ExpressionView package contains two independent parts: An ordering algorithm implemented in C++ and an Adobe Flash applet written in ActionScript and Adobe Flex. These two programs are wrapped in an R package, allowing the user to take advantage of the powerful microarray analysis tools provided by the Bioconductor project. The Flash applet itself does not require a working R environment, it can be launched in any web browser via the links provided below. If you prefer a stand-alone program, you can also download the platform independent Adobe AIR version. <br />
<br />
== Launch the ExpressionView Flash applet == <br />
* [http://www2.unil.ch/cbg/software/expressionview/flash/ExpressionView.html Launch ExpressionView]<br />
* [http://www2.unil.ch/cbg/software/expressionview/flash/ExpressionView.html?filename=../data/Expressionview.sampledata.all.small.evf Launch ExpressionView with adult T-cell acute lymphocytic leukemia (ALL) data (8 modules)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/flash/ExpressionView.html?filename=../data/Expressionview.sampledata.all.large.evf Launch ExpressionView with adult T-cell acute lymphocytic leukemia (ALL) data (108 modules)]<br />
<br />
== Download the R package (includes the Flash applet) ==<br />
* [http://www2.unil.ch/cbg/software/expressionview/r/ExpressionView_0.2.1_windows.zip Windows binary package]<br />
* [http://www2.unil.ch/cbg/software/expressionview/r/ExpressionView_0.2.1_macosx_32.tar.gz Mac OS X 32 bit binary package], [http://www2.unil.ch/cbg/software/expressionview/r/ExpressionView_0.2.1_macosx_64.tar.gz Mac OS X 64 bit binary package]<br />
* [http://www2.unil.ch/cbg/software/expressionview/r/ExpressionView_0.2.1_source.tar.gz Source package]<br />
Note that ExpressionView requires the '''[[ISA|ISA package]]'''.<br />
<br />
== Download the stand-alone viewer (Adobe AIR) ==<br />
If you prefer a stand-alone viewer, you can download and install the Adobe AIR build [http://www2.unil.ch/cbg/software/expressionview/air/ExpressionView.air ExpressionView.air] (right-click to download file).<br><br />
To run the program, you need the AIR runtime environment which you can get from [http://get.adobe.com/air Adobe].<br><br />
ExpressionView creates files associations to .evf files, allowing you to simply double-click on such files to launch the viewer and load the data.<br />
<br />
== Download sample data ==<br />
* [http://www2.unil.ch/cbg/software/expressionview/data/Expressionview.sampledata.all.small.evf Gene expression profile of adult T-cell acute lymphocytic leukemia (ALL) with 8 modules] (right-click to download file).<br />
* [http://www2.unil.ch/cbg/software/expressionview/Expressionview.sampledata.all.large.evf Gene expression profile of adult T-cell acute lymphocytic leukemia (ALL) with 108 modules] (right-click to download file).<br />
<br />
= Screenshots = <br />
<gallery widths="200px" heights="109px" perrow="3"><br />
image:Expressionview.screenshot.1.png|Startup screen<br />
image:Expressionview.screenshot.2.png|Global view after loading dataset<br />
image:Expressionview.screenshot.3.png|Highlighting modules<br />
image:Expressionview.screenshot.4.png|Zoom functions<br />
image:Expressionview.screenshot.5.png|Highlighting genes (probes) and samples<br />
image:Expressionview.screenshot.6.png|GO and KEGG associations<br />
image:Expressionview.screenshot.7.png|Modules view emphasizing the underlying gene expression data<br />
image:Expressionview.screenshot.8.png|Global view without gene expression data<br />
image:Expressionview.screenshot.9.png|Experiment description<br />
</gallery><br />
<br />
= Tutorials =<br />
There are several tutorials describing how to use ExpressionView. The features of the R package are documented within the program. Just have a look at the ExpressionView help page after you have installed the package. Below, you can download the tutorial presenting the basic workflow and the description of the ordering algorithm. For the Flash applet, we have produced a few videos showing you how to use the program. <br />
<br />
== R package ==<br />
* [[Media:Expressionview.tutorial.pdf|Getting started with ExpressionView]]<br />
* [[Media:Expressionview.ordering.pdf|Ordering algorithm]]<br />
<br />
== Flash applet ==<br />
* [[Media:Expressionview.quickhelp.pdf|Quick help (pdf)]]<br />
<br />
<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.getting.started.mov Getting started (video tutorial, 6 minutes)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.tables.mov Using the tables (video tutorial, 6 minutes)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.modularview.mov Modular view (video tutoria, 4 minutesl)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.view.mov Fullscreen feature (video tutorial, 1 minute)]<br />
<br />
== Installing the stand-alone version == <br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.standalone.mov Stand-alone installation (video tutorial, 2 minutes)]<br />
<br />
= Additional documentation and downloads =<br />
The Flash applet is written in ActionScript. It is open source and can be built from the command line using the Adobe Flex SDK or more conveniently with the Adobe Flex Builder IDE. For more information, visit the [http://www.adobe.com/flex Flex website].<br />
* [http://www2.unil.ch/cbg/software/expressionview/source/ExpressionView.tar.gz ExpressionView source code (for the Flash applet)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/doc ActionScript source code documentation]<br />
* [[Media:Expressionview.xmldescription.pdf|Documentation of the XML file structure]]<br />
<br />
For the Flash applet, we have implemented components that could also be used in other applications. The most important one being the LargeBitmapData class that allows one to work with BitmapData of arbitrary size. In the [http://livedocs.adobe.com/flex/3/langref/flash/display/BitmapData.html standard BitmapData class], the maximum size for a BitmapData object is 8,192 pixels in width or height, and the total number of pixels cannot exceed 16,777,216 pixels. Note that the ResizablePanel class is no longer used in ExpressionView. <br />
* [[Media:Expressionview.largebitmapdata.tar.gz|ActionScript implementation of the LargeBitmapData class (allows to use bitmaps of arbitrary dimensions)]]<br />
* [[Media:Expressionview.resizablepanel.tar.gz|ActionScript implementation of the ResizablePanel class (a panel with open, maximize, minimize, close and resize buttons)]]</div>Andreashttp://www2.unil.ch/cbg/index.php?title=ExpressionViewExpressionView2009-12-03T07:54:01Z<p>Andreas: /* Additional documentation and downloads */</p>
<hr />
<div>[[image:Expressionview.screenshot.png|Screenshot of the ExpressionView applet|500px|left]]<br />
<br style="clear: both" /><br />
<br><br />
ExpressionView is an R package that provides an interactive environment to explore biclusters identified in gene expression data. A sophisticated ordering algorithm is used to present the biclusters in a visually appealing layout. From this overview, the user can select individual biclusters and access all the biologically relevant data associated with it. The package is aimed to facilitate the collaboration between bioinformaticians and life scientists who are not familiar with the R language.<br />
<br />
= Launch and download =<br />
The ExpressionView package contains two independent parts: An ordering algorithm implemented in C++ and an Adobe Flash applet written in ActionScript and Adobe Flex. These two programs are wrapped in an R package, allowing the user to take advantage of the powerful microarray analysis tools provided by the Bioconductor project. The Flash applet itself does not require a working R environment, it can be launched in any web browser via the links provided below. If you prefer a stand-alone program, you can also download the platform independent Adobe AIR version. <br />
<br />
== Launch the ExpressionView Flash applet == <br />
* [http://www2.unil.ch/cbg/software/expressionview/flash/ExpressionView.html Launch ExpressionView]<br />
* [http://www2.unil.ch/cbg/software/expressionview/flash/ExpressionView.html?filename=../data/Expressionview.sampledata.all.small.evf Launch ExpressionView with adult T-cell acute lymphocytic leukemia (ALL) data (8 modules)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/flash/ExpressionView.html?filename=../data/Expressionview.sampledata.all.large.evf Launch ExpressionView with adult T-cell acute lymphocytic leukemia (ALL) data (108 modules)]<br />
<br />
== Download the R package (includes the Flash applet) ==<br />
* [http://www2.unil.ch/cbg/software/expressionview/r/ExpressionView_0.2.1_windows.zip Windows binary package]<br />
* [http://www2.unil.ch/cbg/software/expressionview/r/ExpressionView_0.2.1_macosx_32.tar.gz Mac OS X 32 bit binary package], [http://www2.unil.ch/cbg/software/expressionview/r/ExpressionView_0.2.1_macosx_64.tar.gz Mac OS X 64 bit binary package]<br />
* [http://www2.unil.ch/cbg/software/expressionview/r/ExpressionView_0.2.1_source.tar.gz Source package]<br />
<br />
== Download the stand-alone viewer (Adobe AIR) ==<br />
If you prefer a stand-alone viewer, you can download and install the Adobe AIR build [http://www2.unil.ch/cbg/software/expressionview/air/ExpressionView.air ExpressionView.air] (right-click to download file).<br><br />
To run the program, you need the AIR runtime environment which you can get from [http://get.adobe.com/air Adobe].<br><br />
ExpressionView creates files associations to .evf files, allowing you to simply double-click on such files to launch the viewer and load the data.<br />
<br />
== Download sample data ==<br />
* [http://www2.unil.ch/cbg/software/expressionview/data/Expressionview.sampledata.all.small.evf Gene expression profile of adult T-cell acute lymphocytic leukemia (ALL) with 8 modules] (right-click to download file).<br />
* [http://www2.unil.ch/cbg/software/expressionview/Expressionview.sampledata.all.large.evf Gene expression profile of adult T-cell acute lymphocytic leukemia (ALL) with 108 modules] (right-click to download file).<br />
<br />
= Screenshots = <br />
<gallery widths="200px" heights="109px" perrow="3"><br />
image:Expressionview.screenshot.1.png|Startup screen<br />
image:Expressionview.screenshot.2.png|Global view after loading dataset<br />
image:Expressionview.screenshot.3.png|Highlighting modules<br />
image:Expressionview.screenshot.4.png|Zoom functions<br />
image:Expressionview.screenshot.5.png|Highlighting genes (probes) and samples<br />
image:Expressionview.screenshot.6.png|GO and KEGG associations<br />
image:Expressionview.screenshot.7.png|Modules view emphasizing the underlying gene expression data<br />
image:Expressionview.screenshot.8.png|Global view without gene expression data<br />
image:Expressionview.screenshot.9.png|Experiment description<br />
</gallery><br />
<br />
= Tutorials =<br />
There are several tutorials describing how to use ExpressionView. The features of the R package are documented within the program. Just have a look at the ExpressionView help page after you have installed the package. Below, you can download the tutorial presenting the basic workflow and the description of the ordering algorithm. For the Flash applet, we have produced a few videos showing you how to use the program. <br />
<br />
== R package ==<br />
* [[Media:Expressionview.tutorial.pdf|Getting started with ExpressionView]]<br />
* [[Media:Expressionview.ordering.pdf|Ordering algorithm]]<br />
<br />
== Flash applet ==<br />
* [[Media:Expressionview.quickhelp.pdf|Quick help (pdf)]]<br />
<br />
<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.getting.started.mov Getting started (video tutorial, 6 minutes)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.tables.mov Using the tables (video tutorial, 6 minutes)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.modularview.mov Modular view (video tutoria, 4 minutesl)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.view.mov Fullscreen feature (video tutorial, 1 minute)]<br />
<br />
== Installing the stand-alone version == <br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.standalone.mov Stand-alone installation (video tutorial, 2 minutes)]<br />
<br />
= Additional documentation and downloads =<br />
The Flash applet is written in ActionScript. It is open source and can be built from the command line using the Adobe Flex SDK or more conveniently with the Adobe Flex Builder IDE. For more information, visit the [http://www.adobe.com/flex Flex website].<br />
* [http://www2.unil.ch/cbg/software/expressionview/source/ExpressionView.tar.gz ExpressionView source code (for the Flash applet)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/doc ActionScript source code documentation]<br />
* [[Media:Expressionview.xmldescription.pdf|Documentation of the XML file structure]]<br />
<br />
For the Flash applet, we have implemented components that could also be used in other applications. The most important one being the LargeBitmapData class that allows one to work with BitmapData of arbitrary size. In the [http://livedocs.adobe.com/flex/3/langref/flash/display/BitmapData.html standard BitmapData class], the maximum size for a BitmapData object is 8,192 pixels in width or height, and the total number of pixels cannot exceed 16,777,216 pixels. Note that the ResizablePanel class is no longer used in ExpressionView. <br />
* [[Media:Expressionview.largebitmapdata.tar.gz|ActionScript implementation of the LargeBitmapData class (allows to use bitmaps of arbitrary dimensions)]]<br />
* [[Media:Expressionview.resizablepanel.tar.gz|ActionScript implementation of the ResizablePanel class (a panel with open, maximize, minimize, close and resize buttons)]]</div>Andreashttp://www2.unil.ch/cbg/index.php?title=ExpressionViewExpressionView2009-12-03T07:30:20Z<p>Andreas: </p>
<hr />
<div>[[image:Expressionview.screenshot.png|Screenshot of the ExpressionView applet|500px|left]]<br />
<br style="clear: both" /><br />
<br><br />
ExpressionView is an R package that provides an interactive environment to explore biclusters identified in gene expression data. A sophisticated ordering algorithm is used to present the biclusters in a visually appealing layout. From this overview, the user can select individual biclusters and access all the biologically relevant data associated with it. The package is aimed to facilitate the collaboration between bioinformaticians and life scientists who are not familiar with the R language.<br />
<br />
= Launch and download =<br />
The ExpressionView package contains two independent parts: An ordering algorithm implemented in C++ and an Adobe Flash applet written in ActionScript and Adobe Flex. These two programs are wrapped in an R package, allowing the user to take advantage of the powerful microarray analysis tools provided by the Bioconductor project. The Flash applet itself does not require a working R environment, it can be launched in any web browser via the links provided below. If you prefer a stand-alone program, you can also download the platform independent Adobe AIR version. <br />
<br />
== Launch the ExpressionView Flash applet == <br />
* [http://www2.unil.ch/cbg/software/expressionview/flash/ExpressionView.html Launch ExpressionView]<br />
* [http://www2.unil.ch/cbg/software/expressionview/flash/ExpressionView.html?filename=../data/Expressionview.sampledata.all.small.evf Launch ExpressionView with adult T-cell acute lymphocytic leukemia (ALL) data (8 modules)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/flash/ExpressionView.html?filename=../data/Expressionview.sampledata.all.large.evf Launch ExpressionView with adult T-cell acute lymphocytic leukemia (ALL) data (108 modules)]<br />
<br />
== Download the R package (includes the Flash applet) ==<br />
* [http://www2.unil.ch/cbg/software/expressionview/r/ExpressionView_0.2.1_windows.zip Windows binary package]<br />
* [http://www2.unil.ch/cbg/software/expressionview/r/ExpressionView_0.2.1_macosx_32.tar.gz Mac OS X 32 bit binary package], [http://www2.unil.ch/cbg/software/expressionview/r/ExpressionView_0.2.1_macosx_64.tar.gz Mac OS X 64 bit binary package]<br />
* [http://www2.unil.ch/cbg/software/expressionview/r/ExpressionView_0.2.1_source.tar.gz Source package]<br />
<br />
== Download the stand-alone viewer (Adobe AIR) ==<br />
If you prefer a stand-alone viewer, you can download and install the Adobe AIR build [http://www2.unil.ch/cbg/software/expressionview/air/ExpressionView.air ExpressionView.air] (right-click to download file).<br><br />
To run the program, you need the AIR runtime environment which you can get from [http://get.adobe.com/air Adobe].<br><br />
ExpressionView creates files associations to .evf files, allowing you to simply double-click on such files to launch the viewer and load the data.<br />
<br />
== Download sample data ==<br />
* [http://www2.unil.ch/cbg/software/expressionview/data/Expressionview.sampledata.all.small.evf Gene expression profile of adult T-cell acute lymphocytic leukemia (ALL) with 8 modules] (right-click to download file).<br />
* [http://www2.unil.ch/cbg/software/expressionview/Expressionview.sampledata.all.large.evf Gene expression profile of adult T-cell acute lymphocytic leukemia (ALL) with 108 modules] (right-click to download file).<br />
<br />
= Screenshots = <br />
<gallery widths="200px" heights="109px" perrow="3"><br />
image:Expressionview.screenshot.1.png|Startup screen<br />
image:Expressionview.screenshot.2.png|Global view after loading dataset<br />
image:Expressionview.screenshot.3.png|Highlighting modules<br />
image:Expressionview.screenshot.4.png|Zoom functions<br />
image:Expressionview.screenshot.5.png|Highlighting genes (probes) and samples<br />
image:Expressionview.screenshot.6.png|GO and KEGG associations<br />
image:Expressionview.screenshot.7.png|Modules view emphasizing the underlying gene expression data<br />
image:Expressionview.screenshot.8.png|Global view without gene expression data<br />
image:Expressionview.screenshot.9.png|Experiment description<br />
</gallery><br />
<br />
= Tutorials =<br />
There are several tutorials describing how to use ExpressionView. The features of the R package are documented within the program. Just have a look at the ExpressionView help page after you have installed the package. Below, you can download the tutorial presenting the basic workflow and the description of the ordering algorithm. For the Flash applet, we have produced a few videos showing you how to use the program. <br />
<br />
== R package ==<br />
* [[Media:Expressionview.tutorial.pdf|Getting started with ExpressionView]]<br />
* [[Media:Expressionview.ordering.pdf|Ordering algorithm]]<br />
<br />
== Flash applet ==<br />
* [[Media:Expressionview.quickhelp.pdf|Quick help (pdf)]]<br />
<br />
<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.getting.started.mov Getting started (video tutorial, 6 minutes)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.tables.mov Using the tables (video tutorial, 6 minutes)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.modularview.mov Modular view (video tutoria, 4 minutesl)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.view.mov Fullscreen feature (video tutorial, 1 minute)]<br />
<br />
== Installing the stand-alone version == <br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.standalone.mov Stand-alone installation (video tutorial, 2 minutes)]<br />
<br />
= Additional documentation and downloads =<br />
The Flash applet is written in ActionScript. It is open source and can be built from the command line using the Adobe Flex SDK or more conveniently with the Adobe Flex Builder IDE. For more information, visit the [http://www.adobe.com/flex Flex website].<br />
* [http://www2.unil.ch/cbg/software/expressionview/source/ExpressionView.tar.gz ExpressionView source code (for the Flash applet)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/doc ActionScript source code documentation]<br />
* [[Media:Expressionview.largebitmapdata.tar.gz|ActionScript implementation of the LargeBitmapData class (allows to use bitmaps of arbitrary dimensions)]]<br />
* [[Media:Expressionview.resizablepanel.tar.gz|ActionScript implementation of the ResizablePanel class (a panel with open, maximize, minimize, close and resize buttons)]]<br />
<br />
* [[Media:Expressionview.xmldescription.pdf|Documentation of the XML file structure]]</div>Andreashttp://www2.unil.ch/cbg/index.php?title=ExpressionViewExpressionView2009-12-03T07:23:32Z<p>Andreas: </p>
<hr />
<div>[[image:Expressionview.screenshot.png|Screenshot of the ExpressionView applet|500px|left]]<br />
<br style="clear: both" /><br />
<br><br />
ExpressionView is an R package that provides an interactive environment to explore biclusters identified in gene expression data. A sophisticated ordering algorithm is used to present the biclusters in a visually appealing layout. From this overview, the user can select individual biclusters and access all the biologically relevant data associated with it. The package is aimed to facilitate the collaboration between bioinformaticians and life scientists who are not familiar with the R language.<br />
<br />
= Launch and download =<br />
The ExpressionView package contains two independent parts: An ordering algorithm implemented in C++ and an Adobe Flash applet written in ActionScript and Adobe Flex. These two programs are wrapped in an R package, allowing the user to take advantage of the powerful microarray analysis tools provided by the Bioconductor project. The Flash applet itself does not require a working R environment, it can be launched in any web browser via the links provided below. If you prefer a stand-alone program, you can also download the platform independent Adobe AIR version. <br />
<br />
== Launch the ExpressionView Flash applet == <br />
* [http://www2.unil.ch/cbg/software/expressionview/flash/ExpressionView.html Launch ExpressionView]<br />
* [http://www2.unil.ch/cbg/software/expressionview/flash/ExpressionView.html?filename=../data/Expressionview.sampledata.all.small.evf Launch ExpressionView with adult T-cell acute lymphocytic leukemia (ALL) data (8 modules)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/flash/ExpressionView.html?filename=../data/Expressionview.sampledata.all.large.evf Launch ExpressionView with adult T-cell acute lymphocytic leukemia (ALL) data (108 modules)]<br />
<br />
== Download the R package (includes the Flash applet) ==<br />
* [http://www2.unil.ch/cbg/software/expressionview/r/ExpressionView_0.2.1_windows.zip Windows binary package]<br />
* [http://www2.unil.ch/cbg/software/expressionview/r/ExpressionView_0.2.1_macosx_32.tar.gz Mac OS X 32 bit binary package], [http://www2.unil.ch/cbg/software/expressionview/r/ExpressionView_0.2.1_macosx_64.tar.gz Mac OS X 64 bit binary package]<br />
* [http://www2.unil.ch/cbg/software/expressionview/r/ExpressionView_0.2.1_source.tar.gz Source package]<br />
<br />
== Download the stand-alone viewer (Adobe AIR) ==<br />
If you prefer a stand-alone viewer, you can download and install the Adobe AIR build [http://www2.unil.ch/cbg/software/expressionview/air/ExpressionView.air ExpressionView.air] (right-click to download file).<br><br />
To run the program, you need the AIR runtime environment which you can get from [http://get.adobe.com/air Adobe].<br><br />
ExpressionView creates files associations to .evf files, allowing you to simply double-click on such files to launch the viewer and load the data.<br />
<br />
== Download sample data ==<br />
* [http://www2.unil.ch/cbg/software/expressionview/data/Expressionview.sampledata.all.small.evf Gene expression profile of adult T-cell acute lymphocytic leukemia (ALL) with 8 modules] (right-click to download file).<br />
* [http://www2.unil.ch/cbg/software/expressionview/Expressionview.sampledata.all.large.evf Gene expression profile of adult T-cell acute lymphocytic leukemia (ALL) with 108 modules] (right-click to download file).<br />
<br />
= Screenshots = <br />
<gallery widths="200px" heights="109px" perrow="3"><br />
image:Expressionview.screenshot.1.png|Startup screen<br />
image:Expressionview.screenshot.2.png|Global view after loading dataset<br />
image:Expressionview.screenshot.3.png|Highlighting modules<br />
image:Expressionview.screenshot.4.png|Zoom functions<br />
image:Expressionview.screenshot.5.png|Highlighting genes (probes) and samples<br />
image:Expressionview.screenshot.6.png|GO and KEGG associations<br />
image:Expressionview.screenshot.7.png|Modules view emphasizing the underlying gene expression data<br />
image:Expressionview.screenshot.8.png|Global view without gene expression data<br />
image:Expressionview.screenshot.9.png|Experiment description<br />
</gallery><br />
<br />
= Tutorials =<br />
There are several tutorials describing how to use ExpressionView. The features of the R package are documented within the program. Just have a look at the ExpressionView help page after you have installed the package. Below, you can download the tutorial presenting the basic workflow and the description of the ordering algorithm. For the Flash applet, we have produced a few videos showing you how to use the program. <br />
<br />
== R package ==<br />
* [[Media:Expressionview.tutorial.pdf|Getting started with ExpressionView]]<br />
* [[Media:Expressionview.ordering.pdf|Ordering algorithm]]<br />
<br />
== Flash applet ==<br />
* [[Media:Expressionview.quickhelp.pdf|Quick help (pdf)]]<br />
<br />
<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.getting.started.mov Getting started (video tutorial, 6 minutes)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.tables.mov Using the tables (video tutorial, 6 minutes)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.modularview.mov Modular view (video tutoria, 4 minutesl)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.view.mov Fullscreen feature (video tutorial, 1 minute)]<br />
<br />
== Installing the stand-alone version == <br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.standalone.mov Stand-alone installation (video tutorial, 2 minutes)]<br />
<br />
= Additional documentation and downloads =<br />
The Flash applet is written in ActionScript. It is open source and can be built on the command line with the Adobe Flex SDK or more conveniently with Adobe Flex Builder IDE. For more information, visit the [[http://www.adobe.com/flex Flex website]].<br />
* [http://www2.unil.ch/cbg/software/expressionview/doc ActionScript source code documentation]<br />
* [[Media:Expressionview.xmldescription.pdf|XML file structure]]<br />
* [[Media:Expressionview.largebitmapdata.tar.gz|ActionScript implementation of the LargeBitmapData class (allows to use bitmaps of arbitrary dimensions)]]<br />
* [[Media:Expressionview.resizablepanel.tar.gz|ActionScript implementation of the ResizablePanel class (a panel with open, maximize, minimize, close and resize buttons)]]</div>Andreashttp://www2.unil.ch/cbg/index.php?title=ExpressionViewExpressionView2009-12-03T06:21:31Z<p>Andreas: </p>
<hr />
<div>[[image:Expressionview.screenshot.png|Screenshot of the ExpressionView applet|500px|left]]<br />
<br style="clear: both" /><br />
<br><br />
ExpressionView is an R package that provides an interactive environment to explore biclusters identified in gene expression data. A sophisticated ordering algorithm is used to present the biclusters in a visually appealing layout. From this overview, the user can select individual biclusters and access all the biologically relevant data associated with it. The package is aimed to facilitate the collaboration between bioinformaticians and life scientists who are not familiar with the R language.<br />
<br />
= Launch and download =<br />
<br />
== Launch the ExpressionView Flash applet == <br />
* [http://www2.unil.ch/cbg/software/expressionview/flash/ExpressionView.html Launch ExpressionView]<br />
* [http://www2.unil.ch/cbg/software/expressionview/flash/ExpressionView.html?filename=../data/Expressionview.sampledata.all.small.evf Launch ExpressionView with adult T-cell acute lymphocytic leukemia (ALL) data (8 modules)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/flash/ExpressionView.html?filename=../data/Expressionview.sampledata.all.large.evf Launch ExpressionView with adult T-cell acute lymphocytic leukemia (ALL) data (108 modules)]<br />
<br />
== Download the R package (includes the Flash applet) ==<br />
* [http://www2.unil.ch/cbg/software/expressionview/r/ExpressionView_0.2.1_windows.zip Windows binary package]<br />
* [http://www2.unil.ch/cbg/software/expressionview/r/ExpressionView_0.2.1_macosx_32.tar.gz Mac OS X 32 bit binary package], [http://www2.unil.ch/cbg/software/expressionview/r/ExpressionView_0.2.1_macosx_64.tar.gz Mac OS X 64 bit binary package]<br />
* [http://www2.unil.ch/cbg/software/expressionview/r/ExpressionView_0.2.1_source.tar.gz Source package]<br />
<br />
== Download the stand-alone viewer (Adobe AIR) ==<br />
If you prefer a stand-alone viewer, you can download and install the Adobe AIR build [http://www2.unil.ch/cbg/software/expressionview/air/ExpressionView.air ExpressionView.air] (right-click to download file).<br><br />
To run the program, you need the AIR runtime environment which you can get from [http://get.adobe.com/air Adobe].<br><br />
ExpressionView creates files associations to .evf files, allowing you to simply double-click on such files to launch the viewer and load the data.<br />
<br />
== Download sample data ==<br />
* [http://www2.unil.ch/cbg/software/expressionview/data/Expressionview.sampledata.all.small.evf Gene expression profile of adult T-cell acute lymphocytic leukemia (ALL) with 8 modules] (right-click to download file).<br />
* [http://www2.unil.ch/cbg/software/expressionview/Expressionview.sampledata.all.large.evf Gene expression profile of adult T-cell acute lymphocytic leukemia (ALL) with 108 modules] (right-click to download file).<br />
<br />
= Screenshots = <br />
<gallery widths="200px" heights="109px" perrow="3"><br />
image:Expressionview.screenshot.1.png|Startup screen<br />
image:Expressionview.screenshot.2.png|Global view after loading dataset<br />
image:Expressionview.screenshot.3.png|Highlighting modules<br />
image:Expressionview.screenshot.4.png|Zoom functions<br />
image:Expressionview.screenshot.5.png|Highlighting genes (probes) and samples<br />
image:Expressionview.screenshot.6.png|GO and KEGG associations<br />
image:Expressionview.screenshot.7.png|Modules view emphasizing the underlying gene expression data<br />
image:Expressionview.screenshot.8.png|Global view without gene expression data<br />
image:Expressionview.screenshot.9.png|Experiment description<br />
</gallery><br />
<br />
= Tutorials =<br />
There are several tutorials describing how to use ExpressionView:<br />
<br />
== R package ==<br />
* [[Media:Expressionview.tutorial.pdf|Getting started with ExpressionView]]<br />
* [[Media:Expressionview.ordering.pdf|Ordering algorithm]]<br />
<br />
== Flash applet ==<br />
* [[Media:Expressionview.quickhelp.pdf|Quick help (pdf)]]<br />
<br />
<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.getting.started.mov Getting started (video tutorial, 6 minutes)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.tables.mov Using the tables (video tutorial, 6 minutes)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.modularview.mov Modular view (video tutoria, 4 minutesl)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.view.mov Fullscreen feature (video tutorial, 1 minute)]<br />
<br />
== Installing the stand-alone version == <br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.standalone.mov Stand-alone installation (video tutorial, 2 minutes)]<br />
<br />
= Additional documentation and downloads =<br />
* [http://www2.unil.ch/cbg/software/expressionview/doc ActionScript source code documentation]<br />
* [[Media:Expressionview.xmldescription.pdf|XML file structure]]<br />
* [[Media:Expressionview.largebitmapdata.tar.gz|ActionScript implementation of the LargeBitmapData class (allows to use bitmaps of arbitrary dimensions)]]<br />
* [[Media:Expressionview.resizablepanel.tar.gz|ActionScript implementation of the ResizablePanel class (a panel with open, maximize, minimize, close and resize buttons)]]</div>Andreashttp://www2.unil.ch/cbg/index.php?title=ExpressionViewExpressionView2009-12-03T06:12:29Z<p>Andreas: /* Flash applet */</p>
<hr />
<div>[[image:Expressionview.screenshot.png|Screenshot of the ExpressionView applet|500px|left]]<br />
<br style="clear: both" /><br />
<br><br />
ExpressionView is an R package that provides an interactive environment to explore biclusters identified in gene expression data. A sophisticated ordering algorithm is used to present the biclusters in a visually appealing layout. From this overview, the user can select individual biclusters and access all the biologically relevant data associated with it. The package is aimed to facilitate the collaboration between bioinformaticians and life scientists who are not familiar with the R language.<br />
<br />
= Launch and download =<br />
<br />
== Launch the ExpressionView Flash applet == <br />
* [http://www2.unil.ch/cbg/software/expressionview/flash/ExpressionView.html Launch ExpressionView]<br />
* [http://www2.unil.ch/cbg/software/expressionview/flash/ExpressionView.html?filename=../data/Expressionview.sampledata.all.small.evf Launch ExpressionView with adult T-cell acute lymphocytic leukemia (ALL) data (8 modules)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/flash/ExpressionView.html?filename=../data/Expressionview.sampledata.all.large.evf Launch ExpressionView with adult T-cell acute lymphocytic leukemia (ALL) data (108 modules)]<br />
<br />
== Download the R package (includes the Flash applet) ==<br />
* [http://www2.unil.ch/cbg/software/expressionview/r/ExpressionView_0.2.1_windows.zip Windows binary package]<br />
* [http://www2.unil.ch/cbg/software/expressionview/r/ExpressionView_0.2.1_macosx_32.tar.gz Mac OS X 32 bit binary package], [http://www2.unil.ch/cbg/software/expressionview/r/ExpressionView_0.2.1_macosx_64.tar.gz Mac OS X 64 bit binary package]<br />
* [http://www2.unil.ch/cbg/software/expressionview/r/ExpressionView_0.2.1_source.tar.gz Source package]<br />
<br />
== Download the stand-alone viewer (adobe AIR) ==<br />
If you prefer a stand-alone viewer, you can download and install the Adobe AIR build [http://www2.unil.ch/cbg/software/expressionview/air/ExpressionView.air ExpressionView.air] (right-click to download file).<br><br />
To run the program, you need the AIR runtime environment which you can get from [http://get.adobe.com/air Adobe].<br><br />
ExpressionView creates files associations to .evf files, allowing you to simply double-click on such files to launch the viewer and load the data.<br />
<br />
== Download sample data ==<br />
* [http://www2.unil.ch/cbg/software/expressionview/data/Expressionview.sampledata.all.small.evf Gene expression profile of adult T-cell acute lymphocytic leukemia (ALL) with 8 modules] (right-click to download file).<br />
* [http://www2.unil.ch/cbg/software/expressionview/Expressionview.sampledata.all.large.evf Gene expression profile of adult T-cell acute lymphocytic leukemia (ALL) with 108 modules] (right-click to download file).<br />
<br />
= Screenshots = <br />
<gallery widths="200px" heights="109px" perrow="3"><br />
image:Expressionview.screenshot.1.png|Startup screen<br />
image:Expressionview.screenshot.2.png|Global view after loading dataset<br />
image:Expressionview.screenshot.3.png|Highlighting modules<br />
image:Expressionview.screenshot.4.png|Zoom functions<br />
image:Expressionview.screenshot.5.png|Highlighting genes (probes) and samples<br />
image:Expressionview.screenshot.6.png|GO and KEGG associations<br />
image:Expressionview.screenshot.7.png|Modules view emphasizing the underlying gene expression data<br />
image:Expressionview.screenshot.8.png|Global view without gene expression data<br />
image:Expressionview.screenshot.9.png|Experiment description<br />
</gallery><br />
<br />
= Tutorials =<br />
There are several tutorials describing how to use ExpressionView:<br />
<br />
== R package ==<br />
* [[Media:Expressionview.tutorial.pdf|Getting started with ExpressionView]]<br />
* [[Media:Expressionview.ordering.pdf|Ordering algorithm]]<br />
<br />
== Flash applet ==<br />
* [[Media:Expressionview.quickhelp.pdf|Quick help (pdf)]]<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.getting.started.mov Getting started (video tutorial)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.tables.mov Using the tables (video tutorial)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.modularview.mov Modular view (video tutorial)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.view.mov View and Export functions (video tutorial)]<br />
<br />
== Installing the stand-alone version == <br />
<br />
= Additional documentation and downloads =<br />
* [http://www2.unil.ch/cbg/software/expressionview/doc ActionScript source code documentation]<br />
* [[Media:Expressionview.xmldescription.pdf|XML file structure]]<br />
* [[Media:Expressionview.largebitmapdata.tar.gz|ActionScript implementation of the LargeBitmapData class (allows to use bitmaps of arbitrary dimensions)]]<br />
* [[Media:Expressionview.resizablepanel.tar.gz|ActionScript implementation of the ResizablePanel class (a panel with open, maximize, minimize, close and resize buttons)]]</div>Andreashttp://www2.unil.ch/cbg/index.php?title=ExpressionViewExpressionView2009-12-03T06:11:27Z<p>Andreas: /* Flash applet */</p>
<hr />
<div>[[image:Expressionview.screenshot.png|Screenshot of the ExpressionView applet|500px|left]]<br />
<br style="clear: both" /><br />
<br><br />
ExpressionView is an R package that provides an interactive environment to explore biclusters identified in gene expression data. A sophisticated ordering algorithm is used to present the biclusters in a visually appealing layout. From this overview, the user can select individual biclusters and access all the biologically relevant data associated with it. The package is aimed to facilitate the collaboration between bioinformaticians and life scientists who are not familiar with the R language.<br />
<br />
= Launch and download =<br />
<br />
== Launch the ExpressionView Flash applet == <br />
* [http://www2.unil.ch/cbg/software/expressionview/flash/ExpressionView.html Launch ExpressionView]<br />
* [http://www2.unil.ch/cbg/software/expressionview/flash/ExpressionView.html?filename=../data/Expressionview.sampledata.all.small.evf Launch ExpressionView with adult T-cell acute lymphocytic leukemia (ALL) data (8 modules)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/flash/ExpressionView.html?filename=../data/Expressionview.sampledata.all.large.evf Launch ExpressionView with adult T-cell acute lymphocytic leukemia (ALL) data (108 modules)]<br />
<br />
== Download the R package (includes the Flash applet) ==<br />
* [http://www2.unil.ch/cbg/software/expressionview/r/ExpressionView_0.2.1_windows.zip Windows binary package]<br />
* [http://www2.unil.ch/cbg/software/expressionview/r/ExpressionView_0.2.1_macosx_32.tar.gz Mac OS X 32 bit binary package], [http://www2.unil.ch/cbg/software/expressionview/r/ExpressionView_0.2.1_macosx_64.tar.gz Mac OS X 64 bit binary package]<br />
* [http://www2.unil.ch/cbg/software/expressionview/r/ExpressionView_0.2.1_source.tar.gz Source package]<br />
<br />
== Download the stand-alone viewer (adobe AIR) ==<br />
If you prefer a stand-alone viewer, you can download and install the Adobe AIR build [http://www2.unil.ch/cbg/software/expressionview/air/ExpressionView.air ExpressionView.air] (right-click to download file).<br><br />
To run the program, you need the AIR runtime environment which you can get from [http://get.adobe.com/air Adobe].<br><br />
ExpressionView creates files associations to .evf files, allowing you to simply double-click on such files to launch the viewer and load the data.<br />
<br />
== Download sample data ==<br />
* [http://www2.unil.ch/cbg/software/expressionview/data/Expressionview.sampledata.all.small.evf Gene expression profile of adult T-cell acute lymphocytic leukemia (ALL) with 8 modules] (right-click to download file).<br />
* [http://www2.unil.ch/cbg/software/expressionview/Expressionview.sampledata.all.large.evf Gene expression profile of adult T-cell acute lymphocytic leukemia (ALL) with 108 modules] (right-click to download file).<br />
<br />
= Screenshots = <br />
<gallery widths="200px" heights="109px" perrow="3"><br />
image:Expressionview.screenshot.1.png|Startup screen<br />
image:Expressionview.screenshot.2.png|Global view after loading dataset<br />
image:Expressionview.screenshot.3.png|Highlighting modules<br />
image:Expressionview.screenshot.4.png|Zoom functions<br />
image:Expressionview.screenshot.5.png|Highlighting genes (probes) and samples<br />
image:Expressionview.screenshot.6.png|GO and KEGG associations<br />
image:Expressionview.screenshot.7.png|Modules view emphasizing the underlying gene expression data<br />
image:Expressionview.screenshot.8.png|Global view without gene expression data<br />
image:Expressionview.screenshot.9.png|Experiment description<br />
</gallery><br />
<br />
= Tutorials =<br />
There are several tutorials describing how to use ExpressionView:<br />
<br />
== R package ==<br />
* [[Media:Expressionview.tutorial.pdf|Getting started with ExpressionView]]<br />
* [[Media:Expressionview.ordering.pdf|Ordering algorithm]]<br />
<br />
== Flash applet ==<br />
[[Media:Expressionview.quickhelp.pdf|Quick help (pdf)]]<br />
[http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.getting.started.mov Getting started (video tutorial)]<br />
[http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.tables.mov Using the tables (video tutorial)]<br />
[http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.modularview.mov Modular view (video tutorial)]<br />
[http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.view.mov View and Export functions (video tutorial)]<br />
<br />
== Installing the stand-alone version == <br />
<br />
= Additional documentation and downloads =<br />
* [http://www2.unil.ch/cbg/software/expressionview/doc ActionScript source code documentation]<br />
* [[Media:Expressionview.xmldescription.pdf|XML file structure]]<br />
* [[Media:Expressionview.largebitmapdata.tar.gz|ActionScript implementation of the LargeBitmapData class (allows to use bitmaps of arbitrary dimensions)]]<br />
* [[Media:Expressionview.resizablepanel.tar.gz|ActionScript implementation of the ResizablePanel class (a panel with open, maximize, minimize, close and resize buttons)]]</div>Andreashttp://www2.unil.ch/cbg/index.php?title=ExpressionViewExpressionView2009-12-03T05:47:01Z<p>Andreas: /* R package */</p>
<hr />
<div>[[image:Expressionview.screenshot.png|Screenshot of the ExpressionView applet|500px|left]]<br />
<br style="clear: both" /><br />
<br><br />
ExpressionView is an R package that provides an interactive environment to explore biclusters identified in gene expression data. A sophisticated ordering algorithm is used to present the biclusters in a visually appealing layout. From this overview, the user can select individual biclusters and access all the biologically relevant data associated with it. The package is aimed to facilitate the collaboration between bioinformaticians and life scientists who are not familiar with the R language.<br />
<br />
= Launch and download =<br />
<br />
== Launch the ExpressionView Flash applet == <br />
* [http://www2.unil.ch/cbg/software/expressionview/flash/ExpressionView.html Launch ExpressionView]<br />
* [http://www2.unil.ch/cbg/software/expressionview/flash/ExpressionView.html?filename=../data/Expressionview.sampledata.all.small.evf Launch ExpressionView with adult T-cell acute lymphocytic leukemia (ALL) data (8 modules)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/flash/ExpressionView.html?filename=../data/Expressionview.sampledata.all.large.evf Launch ExpressionView with adult T-cell acute lymphocytic leukemia (ALL) data (108 modules)]<br />
<br />
== Download the R package (includes the Flash applet) ==<br />
* [http://www2.unil.ch/cbg/software/expressionview/r/ExpressionView_0.2.1_windows.zip Windows binary package]<br />
* [http://www2.unil.ch/cbg/software/expressionview/r/ExpressionView_0.2.1_macosx_32.tar.gz Mac OS X 32 bit binary package], [http://www2.unil.ch/cbg/software/expressionview/r/ExpressionView_0.2.1_macosx_64.tar.gz Mac OS X 64 bit binary package]<br />
* [http://www2.unil.ch/cbg/software/expressionview/r/ExpressionView_0.2.1_source.tar.gz Source package]<br />
<br />
== Download the stand-alone viewer (adobe AIR) ==<br />
If you prefer a stand-alone viewer, you can download and install the Adobe AIR build [http://www2.unil.ch/cbg/software/expressionview/air/ExpressionView.air ExpressionView.air] (right-click to download file).<br><br />
To run the program, you need the AIR runtime environment which you can get from [http://get.adobe.com/air Adobe].<br><br />
ExpressionView creates files associations to .evf files, allowing you to simply double-click on such files to launch the viewer and load the data.<br />
<br />
== Download sample data ==<br />
* [http://www2.unil.ch/cbg/software/expressionview/data/Expressionview.sampledata.all.small.evf Gene expression profile of adult T-cell acute lymphocytic leukemia (ALL) with 8 modules] (right-click to download file).<br />
* [http://www2.unil.ch/cbg/software/expressionview/Expressionview.sampledata.all.large.evf Gene expression profile of adult T-cell acute lymphocytic leukemia (ALL) with 108 modules] (right-click to download file).<br />
<br />
= Screenshots = <br />
<gallery widths="200px" heights="109px" perrow="3"><br />
image:Expressionview.screenshot.1.png|Startup screen<br />
image:Expressionview.screenshot.2.png|Global view after loading dataset<br />
image:Expressionview.screenshot.3.png|Highlighting modules<br />
image:Expressionview.screenshot.4.png|Zoom functions<br />
image:Expressionview.screenshot.5.png|Highlighting genes (probes) and samples<br />
image:Expressionview.screenshot.6.png|GO and KEGG associations<br />
image:Expressionview.screenshot.7.png|Modules view emphasizing the underlying gene expression data<br />
image:Expressionview.screenshot.8.png|Global view without gene expression data<br />
image:Expressionview.screenshot.9.png|Experiment description<br />
</gallery><br />
<br />
= Tutorials =<br />
There are several tutorials describing how to use ExpressionView:<br />
<br />
== R package ==<br />
* [[Media:Expressionview.tutorial.pdf|Getting started with ExpressionView]]<br />
* [[Media:Expressionview.ordering.pdf|Ordering algorithm]]<br />
<br />
== Flash applet ==<br />
[[Media:Expressionview.quickhelp.pdf|Short description of the ExpressionView features (taken from the tutorial above)]]<br />
<br />
== Installing the stand-alone version == <br />
<br />
= Additional documentation and downloads =<br />
* [http://www2.unil.ch/cbg/software/expressionview/doc ActionScript source code documentation]<br />
* [[Media:Expressionview.xmldescription.pdf|XML file structure]]<br />
* [[Media:Expressionview.largebitmapdata.tar.gz|ActionScript implementation of the LargeBitmapData class (allows to use bitmaps of arbitrary dimensions)]]<br />
* [[Media:Expressionview.resizablepanel.tar.gz|ActionScript implementation of the ResizablePanel class (a panel with open, maximize, minimize, close and resize buttons)]]</div>Andreashttp://www2.unil.ch/cbg/index.php?title=ExpressionViewExpressionView2009-12-03T05:46:35Z<p>Andreas: /* Additional documentation and downloads */</p>
<hr />
<div>[[image:Expressionview.screenshot.png|Screenshot of the ExpressionView applet|500px|left]]<br />
<br style="clear: both" /><br />
<br><br />
ExpressionView is an R package that provides an interactive environment to explore biclusters identified in gene expression data. A sophisticated ordering algorithm is used to present the biclusters in a visually appealing layout. From this overview, the user can select individual biclusters and access all the biologically relevant data associated with it. The package is aimed to facilitate the collaboration between bioinformaticians and life scientists who are not familiar with the R language.<br />
<br />
= Launch and download =<br />
<br />
== Launch the ExpressionView Flash applet == <br />
* [http://www2.unil.ch/cbg/software/expressionview/flash/ExpressionView.html Launch ExpressionView]<br />
* [http://www2.unil.ch/cbg/software/expressionview/flash/ExpressionView.html?filename=../data/Expressionview.sampledata.all.small.evf Launch ExpressionView with adult T-cell acute lymphocytic leukemia (ALL) data (8 modules)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/flash/ExpressionView.html?filename=../data/Expressionview.sampledata.all.large.evf Launch ExpressionView with adult T-cell acute lymphocytic leukemia (ALL) data (108 modules)]<br />
<br />
== Download the R package (includes the Flash applet) ==<br />
* [http://www2.unil.ch/cbg/software/expressionview/r/ExpressionView_0.2.1_windows.zip Windows binary package]<br />
* [http://www2.unil.ch/cbg/software/expressionview/r/ExpressionView_0.2.1_macosx_32.tar.gz Mac OS X 32 bit binary package], [http://www2.unil.ch/cbg/software/expressionview/r/ExpressionView_0.2.1_macosx_64.tar.gz Mac OS X 64 bit binary package]<br />
* [http://www2.unil.ch/cbg/software/expressionview/r/ExpressionView_0.2.1_source.tar.gz Source package]<br />
<br />
== Download the stand-alone viewer (adobe AIR) ==<br />
If you prefer a stand-alone viewer, you can download and install the Adobe AIR build [http://www2.unil.ch/cbg/software/expressionview/air/ExpressionView.air ExpressionView.air] (right-click to download file).<br><br />
To run the program, you need the AIR runtime environment which you can get from [http://get.adobe.com/air Adobe].<br><br />
ExpressionView creates files associations to .evf files, allowing you to simply double-click on such files to launch the viewer and load the data.<br />
<br />
== Download sample data ==<br />
* [http://www2.unil.ch/cbg/software/expressionview/data/Expressionview.sampledata.all.small.evf Gene expression profile of adult T-cell acute lymphocytic leukemia (ALL) with 8 modules] (right-click to download file).<br />
* [http://www2.unil.ch/cbg/software/expressionview/Expressionview.sampledata.all.large.evf Gene expression profile of adult T-cell acute lymphocytic leukemia (ALL) with 108 modules] (right-click to download file).<br />
<br />
= Screenshots = <br />
<gallery widths="200px" heights="109px" perrow="3"><br />
image:Expressionview.screenshot.1.png|Startup screen<br />
image:Expressionview.screenshot.2.png|Global view after loading dataset<br />
image:Expressionview.screenshot.3.png|Highlighting modules<br />
image:Expressionview.screenshot.4.png|Zoom functions<br />
image:Expressionview.screenshot.5.png|Highlighting genes (probes) and samples<br />
image:Expressionview.screenshot.6.png|GO and KEGG associations<br />
image:Expressionview.screenshot.7.png|Modules view emphasizing the underlying gene expression data<br />
image:Expressionview.screenshot.8.png|Global view without gene expression data<br />
image:Expressionview.screenshot.9.png|Experiment description<br />
</gallery><br />
<br />
= Tutorials =<br />
There are several tutorials describing how to use ExpressionView:<br />
<br />
== R package ==<br />
[[Media:Expressionview.tutorial.pdf|Getting started with ExpressionView]]<br />
<br />
== Flash applet ==<br />
[[Media:Expressionview.quickhelp.pdf|Short description of the ExpressionView features (taken from the tutorial above)]]<br />
<br />
== Installing the stand-alone version == <br />
<br />
= Additional documentation and downloads =<br />
* [http://www2.unil.ch/cbg/software/expressionview/doc ActionScript source code documentation]<br />
* [[Media:Expressionview.xmldescription.pdf|XML file structure]]<br />
* [[Media:Expressionview.largebitmapdata.tar.gz|ActionScript implementation of the LargeBitmapData class (allows to use bitmaps of arbitrary dimensions)]]<br />
* [[Media:Expressionview.resizablepanel.tar.gz|ActionScript implementation of the ResizablePanel class (a panel with open, maximize, minimize, close and resize buttons)]]</div>Andreashttp://www2.unil.ch/cbg/index.php?title=File:Expressionview.quickhelp.pdfFile:Expressionview.quickhelp.pdf2009-12-03T05:46:06Z<p>Andreas: Short description of ExpressionView Flash features.</p>
<hr />
<div>Short description of ExpressionView Flash features.</div>Andreashttp://www2.unil.ch/cbg/index.php?title=ExpressionViewExpressionView2009-12-03T05:31:24Z<p>Andreas: </p>
<hr />
<div>[[image:Expressionview.screenshot.png|Screenshot of the ExpressionView applet|500px|left]]<br />
<br style="clear: both" /><br />
<br><br />
ExpressionView is an R package that provides an interactive environment to explore biclusters identified in gene expression data. A sophisticated ordering algorithm is used to present the biclusters in a visually appealing layout. From this overview, the user can select individual biclusters and access all the biologically relevant data associated with it. The package is aimed to facilitate the collaboration between bioinformaticians and life scientists who are not familiar with the R language.<br />
<br />
= Launch and download =<br />
<br />
== Launch the ExpressionView Flash applet == <br />
* [http://www2.unil.ch/cbg/software/expressionview/flash/ExpressionView.html Launch ExpressionView]<br />
* [http://www2.unil.ch/cbg/software/expressionview/flash/ExpressionView.html?filename=../data/Expressionview.sampledata.all.small.evf Launch ExpressionView with adult T-cell acute lymphocytic leukemia (ALL) data (8 modules)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/flash/ExpressionView.html?filename=../data/Expressionview.sampledata.all.large.evf Launch ExpressionView with adult T-cell acute lymphocytic leukemia (ALL) data (108 modules)]<br />
<br />
== Download the R package (includes the Flash applet) ==<br />
* [http://www2.unil.ch/cbg/software/expressionview/r/ExpressionView_0.2.1_windows.zip Windows binary package]<br />
* [http://www2.unil.ch/cbg/software/expressionview/r/ExpressionView_0.2.1_macosx_32.tar.gz Mac OS X 32 bit binary package], [http://www2.unil.ch/cbg/software/expressionview/r/ExpressionView_0.2.1_macosx_64.tar.gz Mac OS X 64 bit binary package]<br />
* [http://www2.unil.ch/cbg/software/expressionview/r/ExpressionView_0.2.1_source.tar.gz Source package]<br />
<br />
== Download the stand-alone viewer (adobe AIR) ==<br />
If you prefer a stand-alone viewer, you can download and install the Adobe AIR build [http://www2.unil.ch/cbg/software/expressionview/air/ExpressionView.air ExpressionView.air] (right-click to download file).<br><br />
To run the program, you need the AIR runtime environment which you can get from [http://get.adobe.com/air Adobe].<br><br />
ExpressionView creates files associations to .evf files, allowing you to simply double-click on such files to launch the viewer and load the data.<br />
<br />
== Download sample data ==<br />
* [http://www2.unil.ch/cbg/software/expressionview/data/Expressionview.sampledata.all.small.evf Gene expression profile of adult T-cell acute lymphocytic leukemia (ALL) with 8 modules] (right-click to download file).<br />
* [http://www2.unil.ch/cbg/software/expressionview/Expressionview.sampledata.all.large.evf Gene expression profile of adult T-cell acute lymphocytic leukemia (ALL) with 108 modules] (right-click to download file).<br />
<br />
= Screenshots = <br />
<gallery widths="200px" heights="109px" perrow="3"><br />
image:Expressionview.screenshot.1.png|Startup screen<br />
image:Expressionview.screenshot.2.png|Global view after loading dataset<br />
image:Expressionview.screenshot.3.png|Highlighting modules<br />
image:Expressionview.screenshot.4.png|Zoom functions<br />
image:Expressionview.screenshot.5.png|Highlighting genes (probes) and samples<br />
image:Expressionview.screenshot.6.png|GO and KEGG associations<br />
image:Expressionview.screenshot.7.png|Modules view emphasizing the underlying gene expression data<br />
image:Expressionview.screenshot.8.png|Global view without gene expression data<br />
image:Expressionview.screenshot.9.png|Experiment description<br />
</gallery><br />
<br />
= Tutorials =<br />
There are several tutorials describing how to use ExpressionView:<br />
<br />
== R package ==<br />
[[Media:Expressionview.tutorial.pdf|Getting started with ExpressionView]]<br />
<br />
== Flash applet ==<br />
[[Media:Expressionview.quickhelp.pdf|Short description of the ExpressionView features (taken from the tutorial above)]]<br />
<br />
== Installing the stand-alone version == <br />
<br />
= Additional documentation and downloads =<br />
* [[Media:Expressionview.ordering.pdf|Ordering algorithm]]<br />
* [hhttp://www2.unil.ch/cbg/software/expressionview/doc ActionScript source code documentation]<br />
* [[Media:Expressionview.xmldescription.pdf|XML file structure]]<br />
* [[Media:Expressionview.largebitmapdata.tar.gz|ActionScript implementation of the LargeBitmapData class (allows to use bitmaps of arbitrary dimensions)]]<br />
* [[Media:Expressionview.resizablepanel.tar.gz|ActionScript implementation of the ResizablePanel class (a panel with open, maximize, minimize, close and resize buttons)]]</div>Andreashttp://www2.unil.ch/cbg/index.php?title=File:Expressionview.tutorial.pdfFile:Expressionview.tutorial.pdf2009-12-03T05:27:06Z<p>Andreas: ExpressionView tutorial</p>
<hr />
<div>ExpressionView tutorial</div>Andreashttp://www2.unil.ch/cbg/index.php?title=ExpressionViewExpressionView2009-12-03T05:19:07Z<p>Andreas: </p>
<hr />
<div>[[image:Expressionview.screenshot.png|Screenshot of the ExpressionView applet|500px|left]]<br />
<br style="clear: both" /><br />
<br><br />
ExpressionView is an R package that provides an interactive environment to explore biclusters identified in gene expression data. A sophisticated ordering algorithm is used to present the biclusters in a visually appealing layout. From this overview, the user can select individual biclusters and access all the biologically relevant data associated with it. The package is aimed to facilitate the collaboration between bioinformaticians and life scientists who are not familiar with the R language.<br />
<br />
= Launch and download =<br />
<br />
== Launch the ExpressionView Flash applet == <br />
* [http://www2.unil.ch/cbg/software/expressionview/flash/ExpressionView.html Launch ExpressionView]<br />
* [http://www2.unil.ch/cbg/software/expressionview/flash/ExpressionView.html?filename=../data/Expressionview.sampledata.all.small.evf Launch ExpressionView with adult T-cell acute lymphocytic leukemia (ALL) data (8 modules)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/flash/ExpressionView.html?filename=../data/Expressionview.sampledata.all.large.evf Launch ExpressionView with adult T-cell acute lymphocytic leukemia (ALL) data (108 modules)]<br />
<br />
== Download the R package (includes the Flash applet) ==<br />
* [http://www2.unil.ch/cbg/software/expressionview/r/ExpressionView_0.2.1_windows.zip Windows binary package]<br />
* [http://www2.unil.ch/cbg/software/expressionview/r/ExpressionView_0.2.1_macosx_32.tar.gz Mac OS X 32 bit binary package], [http://www2.unil.ch/cbg/software/expressionview/r/ExpressionView_0.2.1_macosx_64.tar.gz Mac OS X 64 bit binary package]<br />
* [http://www2.unil.ch/cbg/software/expressionview/r/ExpressionView_0.2.1_source.tar.gz Source package]<br />
<br />
== Download the stand-alone viewer (adobe AIR) ==<br />
If you prefer a stand-alone viewer, you can download and install the Adobe AIR build [http://www2.unil.ch/cbg/software/expressionview/air/ExpressionView.air ExpressionView.air] (right-click to download file).<br><br />
To run the program, you need the AIR runtime environment which you can get from [http://get.adobe.com/air Adobe].<br><br />
ExpressionView creates files associations to .evf files, allowing you to simply double-click on such files to launch the viewer and load the data.<br />
<br />
== Download sample data ==<br />
* [http://www2.unil.ch/cbg/software/expressionview/data/Expressionview.sampledata.all.small.evf Gene expression profile of adult T-cell acute lymphocytic leukemia (ALL) with 8 modules] (right-click to download file).<br />
* [http://www2.unil.ch/cbg/software/expressionview/Expressionview.sampledata.all.large.evf Gene expression profile of adult T-cell acute lymphocytic leukemia (ALL) with 108 modules] (right-click to download file).<br />
<br />
= Screenshots = <br />
<gallery widths="200px" heights="109px" perrow="3"><br />
image:Expressionview.screenshot.1.png|Startup screen<br />
image:Expressionview.screenshot.2.png|Global view after loading dataset<br />
image:Expressionview.screenshot.3.png|Highlighting modules<br />
image:Expressionview.screenshot.4.png|Zoom functions<br />
image:Expressionview.screenshot.5.png|Highlighting genes (probes) and samples<br />
image:Expressionview.screenshot.6.png|GO and KEGG associations<br />
image:Expressionview.screenshot.7.png|Modules view emphasizing the underlying gene expression data<br />
image:Expressionview.screenshot.8.png|Global view without gene expression data<br />
image:Expressionview.screenshot.9.png|Experiment description<br />
</gallery><br />
<br />
= Tutorials =<br />
There are several tutorials describing how to use ExpressionView:<br />
<br />
== R package ==<br />
[[Media:Expressionview.tutorial.pdf|Getting started with ExpressionView]]<br />
<br />
== Flash applet ==<br />
<br />
== Installing the stand-alone version == <br />
<br />
= Additional documentation and downloads =<br />
* [[Media:Expressionview.ordering.pdf|Ordering algorithm]]<br />
* [hhttp://www2.unil.ch/cbg/software/expressionview/doc ActionScript source code documentation]<br />
* [[Media:Expressionview.xmldescription.pdf|XML file structure]]<br />
* [[Media:Expressionview.largebitmapdata.tar.gz|ActionScript implementation of the LargeBitmapData class (allows to use bitmaps of arbitrary dimensions)]]<br />
* [[Media:Expressionview.resizablepanel.tar.gz|ActionScript implementation of the ResizablePanel class (a panel with open, maximize, minimize, close and resize buttons)]]</div>Andreashttp://www2.unil.ch/cbg/index.php?title=ExpressionViewExpressionView2009-11-18T20:35:58Z<p>Andreas: /* Additional documentation and downloads */</p>
<hr />
<div>[[image:Expressionview.screenshot.png|Screenshot of the ExpressionView applet|500px|left]]<br />
<br style="clear: both" /><br />
<br><br />
ExpressionView is an R package that provides an interactive environment to explore biclusters identified in gene expression data. A sophisticated ordering algorithm is used to present the biclusters in a visually appealing layout. From this overview, the user can select individual biclusters and access all the biologically relevant data associated with it. The package is aimed to facilitate the collaboration between bioinformaticians and life scientists who are not familiar with the R language.<br />
<br />
= Launch and download =<br />
<br />
== Launch the ExpressionView Flash applet == <br />
* [http://maya:7575/ExpressionView/bin/ExpressionView.html Launch ExpressionView]<br />
* [http://maya:7575/ExpressionView/bin/ExpressionView.html?filename=../data/Expressionview.sampledata.all.small.evf Launch ExpressionView with adult T-cell acute lymphocytic leukemia (ALL) data (8 modules)]<br />
* [http://maya:7575/ExpressionView/bin/ExpressionView.html?filename=../data/Expressionview.sampledata.all.large.evf Launch ExpressionView with adult T-cell acute lymphocytic leukemia (ALL) data (108 modules)]<br />
<br />
== Download the R package (includes the Flash applet)==<br />
<br />
== Download the stand-alone viewer (adobe AIR) ==<br />
If you prefer a stand-alone viewer, you can download and install the Adobe AIR build [http://maya:7575/ExpressionView/air/ExpressionView.air ExpressionView.air] (right-click to download file).<br><br />
To run the program, you need the AIR runtime environment which you can get from [http://get.adobe.com/air Adobe].<br><br />
ExpressionView creates files associations to .evf files, allowing you to simply double-click on such files to launch the viewer and load the data.<br />
<br />
== Download sample data ==<br />
* [http://maya:7575/ExpressionView/data/Expressionview.sampledata.all.small.evf Gene expression profile of adult T-cell acute lymphocytic leukemia (ALL) with 8 modules] (right-click to download file).<br />
* [http://maya:7575/ExpressionView/Expressionview.sampledata.all.large.evf Gene expression profile of adult T-cell acute lymphocytic leukemia (ALL) with 108 modules] (right-click to download file).<br />
<br />
= Screenshots = <br />
<gallery widths="200px" heights="109px" perrow="3"><br />
image:Expressionview.screenshot.1.png|Startup screen<br />
image:Expressionview.screenshot.2.png|Global view after loading dataset<br />
image:Expressionview.screenshot.3.png|Highlighting modules<br />
image:Expressionview.screenshot.4.png|Zoom functions<br />
image:Expressionview.screenshot.5.png|Highlighting genes (probes) and samples<br />
image:Expressionview.screenshot.6.png|GO and KEGG associations<br />
image:Expressionview.screenshot.7.png|Modules view emphasizing the underlying gene expression data<br />
image:Expressionview.screenshot.8.png|Global view without gene expression data<br />
image:Expressionview.screenshot.9.png|Experiment description<br />
</gallery><br />
<br />
= Tutorials =<br />
There are several tutorials describing how to use ExpressionView:<br />
<br />
== R package ==<br />
<br />
== Flash applet ==<br />
<br />
= Additional documentation and downloads =<br />
* [[Media:Expressionview.ordering.pdf|Ordering algorithm]]<br />
* [http://maya:7575/ExpressionView/doc ActionScript source code documentation]<br />
* [[Media:Expressionview.xmldescription.pdf|XML file structure]]<br />
* [[Media:Expressionview.largebitmapdata.tar.gz|ActionScript implementation of the LargeBitmapData class (allows to use bitmaps of arbitrary dimensions)]]<br />
* [[Media:Expressionview.resizablepanel.tar.gz|ActionScript implementation of the ResizablePanel class (a panel with open, maximize, minimize, close and resize buttons)]]</div>Andreashttp://www2.unil.ch/cbg/index.php?title=File:Expressionview.resizablepanel.tar.gzFile:Expressionview.resizablepanel.tar.gz2009-11-18T20:35:38Z<p>Andreas: ActionScript implementation of the ResizablePanel class that creates panels with open, maximize, minimize, resize and close buttons.</p>
<hr />
<div>ActionScript implementation of the ResizablePanel class that creates panels with open, maximize, minimize, resize and close buttons.</div>Andreashttp://www2.unil.ch/cbg/index.php?title=File:Expressionview.largebitmapdata.tar.gzFile:Expressionview.largebitmapdata.tar.gz2009-11-18T20:34:29Z<p>Andreas: ActionScript implementation of the LargeBitmapData class that allows to handle bitmaps of arbitrary dimensions.</p>
<hr />
<div>ActionScript implementation of the LargeBitmapData class that allows to handle bitmaps of arbitrary dimensions.</div>Andreashttp://www2.unil.ch/cbg/index.php?title=ExpressionViewExpressionView2009-11-18T20:29:43Z<p>Andreas: /* Additional documentation and downloads */</p>
<hr />
<div>[[image:Expressionview.screenshot.png|Screenshot of the ExpressionView applet|500px|left]]<br />
<br style="clear: both" /><br />
<br><br />
ExpressionView is an R package that provides an interactive environment to explore biclusters identified in gene expression data. A sophisticated ordering algorithm is used to present the biclusters in a visually appealing layout. From this overview, the user can select individual biclusters and access all the biologically relevant data associated with it. The package is aimed to facilitate the collaboration between bioinformaticians and life scientists who are not familiar with the R language.<br />
<br />
= Launch and download =<br />
<br />
== Launch the ExpressionView Flash applet == <br />
* [http://maya:7575/ExpressionView/bin/ExpressionView.html Launch ExpressionView]<br />
* [http://maya:7575/ExpressionView/bin/ExpressionView.html?filename=../data/Expressionview.sampledata.all.small.evf Launch ExpressionView with adult T-cell acute lymphocytic leukemia (ALL) data (8 modules)]<br />
* [http://maya:7575/ExpressionView/bin/ExpressionView.html?filename=../data/Expressionview.sampledata.all.large.evf Launch ExpressionView with adult T-cell acute lymphocytic leukemia (ALL) data (108 modules)]<br />
<br />
== Download the R package (includes the Flash applet)==<br />
<br />
== Download the stand-alone viewer (adobe AIR) ==<br />
If you prefer a stand-alone viewer, you can download and install the Adobe AIR build [http://maya:7575/ExpressionView/air/ExpressionView.air ExpressionView.air] (right-click to download file).<br><br />
To run the program, you need the AIR runtime environment which you can get from [http://get.adobe.com/air Adobe].<br><br />
ExpressionView creates files associations to .evf files, allowing you to simply double-click on such files to launch the viewer and load the data.<br />
<br />
== Download sample data ==<br />
* [http://maya:7575/ExpressionView/data/Expressionview.sampledata.all.small.evf Gene expression profile of adult T-cell acute lymphocytic leukemia (ALL) with 8 modules] (right-click to download file).<br />
* [http://maya:7575/ExpressionView/Expressionview.sampledata.all.large.evf Gene expression profile of adult T-cell acute lymphocytic leukemia (ALL) with 108 modules] (right-click to download file).<br />
<br />
= Screenshots = <br />
<gallery widths="200px" heights="109px" perrow="3"><br />
image:Expressionview.screenshot.1.png|Startup screen<br />
image:Expressionview.screenshot.2.png|Global view after loading dataset<br />
image:Expressionview.screenshot.3.png|Highlighting modules<br />
image:Expressionview.screenshot.4.png|Zoom functions<br />
image:Expressionview.screenshot.5.png|Highlighting genes (probes) and samples<br />
image:Expressionview.screenshot.6.png|GO and KEGG associations<br />
image:Expressionview.screenshot.7.png|Modules view emphasizing the underlying gene expression data<br />
image:Expressionview.screenshot.8.png|Global view without gene expression data<br />
image:Expressionview.screenshot.9.png|Experiment description<br />
</gallery><br />
<br />
= Tutorials =<br />
There are several tutorials describing how to use ExpressionView:<br />
<br />
== R package ==<br />
<br />
== Flash applet ==<br />
<br />
= Additional documentation and downloads =<br />
* [[Media:Expressionview.ordering.pdf|Ordering algorithm]]<br />
* [http://maya:7575/ExpressionView/doc ActionScript source code documentation]<br />
* [[Media:Expressionview.xmldescription.pdf|XML file structure]]<br />
* [[Media:Expressionview.largebitmapdata.zip|ActionScript implementation of the LargeBitmapData class (allows to use bitmaps of arbitrary dimensions)]]<br />
* [[Media:Expressionview.resizablepanel.zip|ActionScript implementation of the ResizablePanel class (a panel with open, maximize, minimize, close and resize buttons)]]</div>Andreashttp://www2.unil.ch/cbg/index.php?title=ExpressionViewExpressionView2009-11-18T09:38:04Z<p>Andreas: /* Download the stand-alone viewer (adobe AIR) */</p>
<hr />
<div>[[image:Expressionview.screenshot.png|Screenshot of the ExpressionView applet|500px|left]]<br />
<br style="clear: both" /><br />
<br><br />
ExpressionView is an R package that provides an interactive environment to explore biclusters identified in gene expression data. A sophisticated ordering algorithm is used to present the biclusters in a visually appealing layout. From this overview, the user can select individual biclusters and access all the biologically relevant data associated with it. The package is aimed to facilitate the collaboration between bioinformaticians and life scientists who are not familiar with the R language.<br />
<br />
= Launch and download =<br />
<br />
== Launch the ExpressionView Flash applet == <br />
* [http://maya:7575/ExpressionView/bin/ExpressionView.html Launch ExpressionView]<br />
* [http://maya:7575/ExpressionView/bin/ExpressionView.html?filename=../data/Expressionview.sampledata.all.small.evf Launch ExpressionView with adult T-cell acute lymphocytic leukemia (ALL) data (8 modules)]<br />
* [http://maya:7575/ExpressionView/bin/ExpressionView.html?filename=../data/Expressionview.sampledata.all.large.evf Launch ExpressionView with adult T-cell acute lymphocytic leukemia (ALL) data (108 modules)]<br />
<br />
== Download the R package (includes the Flash applet)==<br />
<br />
== Download the stand-alone viewer (adobe AIR) ==<br />
If you prefer a stand-alone viewer, you can download and install the Adobe AIR build [http://maya:7575/ExpressionView/air/ExpressionView.air ExpressionView.air] (right-click to download file).<br><br />
To run the program, you need the AIR runtime environment which you can get from [http://get.adobe.com/air Adobe].<br><br />
ExpressionView creates files associations to .evf files, allowing you to simply double-click on such files to launch the viewer and load the data.<br />
<br />
== Download sample data ==<br />
* [http://maya:7575/ExpressionView/data/Expressionview.sampledata.all.small.evf Gene expression profile of adult T-cell acute lymphocytic leukemia (ALL) with 8 modules] (right-click to download file).<br />
* [http://maya:7575/ExpressionView/Expressionview.sampledata.all.large.evf Gene expression profile of adult T-cell acute lymphocytic leukemia (ALL) with 108 modules] (right-click to download file).<br />
<br />
= Screenshots = <br />
<gallery widths="200px" heights="109px" perrow="3"><br />
image:Expressionview.screenshot.1.png|Startup screen<br />
image:Expressionview.screenshot.2.png|Global view after loading dataset<br />
image:Expressionview.screenshot.3.png|Highlighting modules<br />
image:Expressionview.screenshot.4.png|Zoom functions<br />
image:Expressionview.screenshot.5.png|Highlighting genes (probes) and samples<br />
image:Expressionview.screenshot.6.png|GO and KEGG associations<br />
image:Expressionview.screenshot.7.png|Modules view emphasizing the underlying gene expression data<br />
image:Expressionview.screenshot.8.png|Global view without gene expression data<br />
image:Expressionview.screenshot.9.png|Experiment description<br />
</gallery><br />
<br />
= Tutorials =<br />
There are several tutorials describing how to use ExpressionView:<br />
<br />
== R package ==<br />
<br />
== Flash applet ==<br />
<br />
= Additional documentation and downloads =<br />
* [[Media:Expressionview.ordering.pdf|Ordering algorithm]]<br />
* [http://maya:7575/ExpressionView/doc ActionScript source code documentation]<br />
* [[Media:Expressionview.xmldescription.pdf|XML file structure]]</div>Andreashttp://www2.unil.ch/cbg/index.php?title=ExpressionViewExpressionView2009-11-18T09:37:39Z<p>Andreas: /* Download sample data */</p>
<hr />
<div>[[image:Expressionview.screenshot.png|Screenshot of the ExpressionView applet|500px|left]]<br />
<br style="clear: both" /><br />
<br><br />
ExpressionView is an R package that provides an interactive environment to explore biclusters identified in gene expression data. A sophisticated ordering algorithm is used to present the biclusters in a visually appealing layout. From this overview, the user can select individual biclusters and access all the biologically relevant data associated with it. The package is aimed to facilitate the collaboration between bioinformaticians and life scientists who are not familiar with the R language.<br />
<br />
= Launch and download =<br />
<br />
== Launch the ExpressionView Flash applet == <br />
* [http://maya:7575/ExpressionView/bin/ExpressionView.html Launch ExpressionView]<br />
* [http://maya:7575/ExpressionView/bin/ExpressionView.html?filename=../data/Expressionview.sampledata.all.small.evf Launch ExpressionView with adult T-cell acute lymphocytic leukemia (ALL) data (8 modules)]<br />
* [http://maya:7575/ExpressionView/bin/ExpressionView.html?filename=../data/Expressionview.sampledata.all.large.evf Launch ExpressionView with adult T-cell acute lymphocytic leukemia (ALL) data (108 modules)]<br />
<br />
== Download the R package (includes the Flash applet)==<br />
<br />
== Download the stand-alone viewer (adobe AIR) ==<br />
If you prefer a stand-alone viewer, you can download and install the Adobe AIR build [http://maya:7575/ExpressionView/air/ExpressionView.air ExpressionView.air].<br><br />
To run the program, you need the AIR runtime environment which you can get from [http://get.adobe.com/air Adobe].<br><br />
ExpressionView creates files associations to .evf files, allowing you to simply double-click on such files to launch the viewer and load the data.<br />
<br />
== Download sample data ==<br />
* [http://maya:7575/ExpressionView/data/Expressionview.sampledata.all.small.evf Gene expression profile of adult T-cell acute lymphocytic leukemia (ALL) with 8 modules] (right-click to download file).<br />
* [http://maya:7575/ExpressionView/Expressionview.sampledata.all.large.evf Gene expression profile of adult T-cell acute lymphocytic leukemia (ALL) with 108 modules] (right-click to download file).<br />
<br />
= Screenshots = <br />
<gallery widths="200px" heights="109px" perrow="3"><br />
image:Expressionview.screenshot.1.png|Startup screen<br />
image:Expressionview.screenshot.2.png|Global view after loading dataset<br />
image:Expressionview.screenshot.3.png|Highlighting modules<br />
image:Expressionview.screenshot.4.png|Zoom functions<br />
image:Expressionview.screenshot.5.png|Highlighting genes (probes) and samples<br />
image:Expressionview.screenshot.6.png|GO and KEGG associations<br />
image:Expressionview.screenshot.7.png|Modules view emphasizing the underlying gene expression data<br />
image:Expressionview.screenshot.8.png|Global view without gene expression data<br />
image:Expressionview.screenshot.9.png|Experiment description<br />
</gallery><br />
<br />
= Tutorials =<br />
There are several tutorials describing how to use ExpressionView:<br />
<br />
== R package ==<br />
<br />
== Flash applet ==<br />
<br />
= Additional documentation and downloads =<br />
* [[Media:Expressionview.ordering.pdf|Ordering algorithm]]<br />
* [http://maya:7575/ExpressionView/doc ActionScript source code documentation]<br />
* [[Media:Expressionview.xmldescription.pdf|XML file structure]]</div>Andreashttp://www2.unil.ch/cbg/index.php?title=ExpressionViewExpressionView2009-11-18T07:29:31Z<p>Andreas: </p>
<hr />
<div>[[image:Expressionview.screenshot.png|Screenshot of the ExpressionView applet|500px|left]]<br />
<br style="clear: both" /><br />
<br><br />
ExpressionView is an R package that provides an interactive environment to explore biclusters identified in gene expression data. A sophisticated ordering algorithm is used to present the biclusters in a visually appealing layout. From this overview, the user can select individual biclusters and access all the biologically relevant data associated with it. The package is aimed to facilitate the collaboration between bioinformaticians and life scientists who are not familiar with the R language.<br />
<br />
= Launch and download =<br />
<br />
== Launch the ExpressionView Flash applet == <br />
* [http://maya:7575/ExpressionView/bin/ExpressionView.html Launch ExpressionView]<br />
* [http://maya:7575/ExpressionView/bin/ExpressionView.html?filename=../data/Expressionview.sampledata.all.small.evf Launch ExpressionView with adult T-cell acute lymphocytic leukemia (ALL) data (8 modules)]<br />
* [http://maya:7575/ExpressionView/bin/ExpressionView.html?filename=../data/Expressionview.sampledata.all.large.evf Launch ExpressionView with adult T-cell acute lymphocytic leukemia (ALL) data (108 modules)]<br />
<br />
== Download the R package (includes the Flash applet)==<br />
<br />
== Download the stand-alone viewer (adobe AIR) ==<br />
If you prefer a stand-alone viewer, you can download and install the Adobe AIR build [http://maya:7575/ExpressionView/air/ExpressionView.air ExpressionView.air].<br><br />
To run the program, you need the AIR runtime environment which you can get from [http://get.adobe.com/air Adobe].<br><br />
ExpressionView creates files associations to .evf files, allowing you to simply double-click on such files to launch the viewer and load the data.<br />
<br />
== Download sample data ==<br />
* [http://maya:7575/ExpressionView/data/Expressionview.sampledata.all.small.evf Gene expression profile of adult T-cell acute lymphocytic leukemia (ALL) with 8 modules]<br />
* [http://maya:7575/ExpressionView/Expressionview.sampledata.all.large.evf Gene expression profile of adult T-cell acute lymphocytic leukemia (ALL) with 108 modules]<br />
<br />
= Screenshots = <br />
<gallery widths="200px" heights="109px" perrow="3"><br />
image:Expressionview.screenshot.1.png|Startup screen<br />
image:Expressionview.screenshot.2.png|Global view after loading dataset<br />
image:Expressionview.screenshot.3.png|Highlighting modules<br />
image:Expressionview.screenshot.4.png|Zoom functions<br />
image:Expressionview.screenshot.5.png|Highlighting genes (probes) and samples<br />
image:Expressionview.screenshot.6.png|GO and KEGG associations<br />
image:Expressionview.screenshot.7.png|Modules view emphasizing the underlying gene expression data<br />
image:Expressionview.screenshot.8.png|Global view without gene expression data<br />
image:Expressionview.screenshot.9.png|Experiment description<br />
</gallery><br />
<br />
= Tutorials =<br />
There are several tutorials describing how to use ExpressionView:<br />
<br />
== R package ==<br />
<br />
== Flash applet ==<br />
<br />
= Additional documentation and downloads =<br />
* [[Media:Expressionview.ordering.pdf|Ordering algorithm]]<br />
* [http://maya:7575/ExpressionView/doc ActionScript source code documentation]<br />
* [[Media:Expressionview.xmldescription.pdf|XML file structure]]</div>Andreashttp://www2.unil.ch/cbg/index.php?title=ExpressionViewExpressionView2009-11-17T22:04:58Z<p>Andreas: </p>
<hr />
<div>[[image:Expressionview.screenshot.png|Screenshot of the ExpressionView applet|500px|left]]<br />
<br style="clear: both" /><br />
<br><br />
ExpressionView is an R package that provides an interactive environment to explore biclusters identified in gene expression data. A sophisticated ordering algorithm is used to present the biclusters in a visually appealing layout. From this overview, the user can select individual biclusters and access all the biologically relevant data associated with it. The package is aimed to facilitate the collaboration between bioinformaticians and life scientists who are not familiar with the R language.<br />
<br />
= Launch and download =<br />
<br />
== Launch the ExpressionView Flash applet == <br />
* [http://maya:7575/ExpressionView/bin/ExpressionView.html Launch ExpressionView]<br />
* [http://maya:7575/ExpressionView/bin/ExpressionView.html?filename=../data/ALL.small.evf Launch ExpressionView with adult T-cell acute lymphocytic leukemia (ALL) data (8 modules)]<br />
* [http://maya:7575/ExpressionView/bin/ExpressionView.html?filename=../data/ALL.large.evf Launch ExpressionView with adult T-cell acute lymphocytic leukemia (ALL) data (108 modules)]<br />
<br />
== Download the R package (includes the Flash applet)==<br />
<br />
== Download the stand-alone viewer (adobe AIR) ==<br />
If you prefer a stand-alone viewer, you can download and install the Adobe AIR build [http://maya:7575/ExpressionView/air/ExpressionView.air ExpressionView.air].<br><br />
To run the program, you need the AIR runtime environment which you can get from [http://get.adobe.com/air Adobe].<br><br />
ExpressionView creates files associations to .evf files, allowing you to simply double-click on such files to launch the viewer and load the data.<br />
<br />
== Download some sample data ==<br />
* [http://maya:7575/ExpressionView/bin/data/Expressionview.sampledata.all.small.evf Gene expression profile of adult T-cell acute lymphocytic leukemia (ALL) with 8 modules]<br />
* [http://maya:7575/ExpressionView/bin/Expressionview.sampledata.all.large.evf Gene expression profile of adult T-cell acute lymphocytic leukemia (ALL) with 108 modules]<br />
<br />
= Screenshots = <br />
<gallery widths="200px" heights="109px" perrow="3"><br />
image:Expressionview.screenshot.1.png|Startup screen<br />
image:Expressionview.screenshot.2.png|Global view after loading dataset<br />
image:Expressionview.screenshot.3.png|Highlighting modules<br />
image:Expressionview.screenshot.4.png|Zoom functions<br />
image:Expressionview.screenshot.5.png|Highlighting genes (probes) and samples<br />
image:Expressionview.screenshot.6.png|GO and KEGG associations<br />
image:Expressionview.screenshot.7.png|Modules view emphasizing the underlying gene expression data<br />
image:Expressionview.screenshot.8.png|Global view without gene expression data<br />
image:Expressionview.screenshot.9.png|Experiment description<br />
</gallery><br />
<br />
= Tutorials =<br />
There are several tutorials describing how to use ExpressionView:<br />
<br />
== R package ==<br />
<br />
== Flash applet ==<br />
<br />
= Additional documentation and downloads =<br />
* [[Media:Expressionview.ordering.pdf|Ordering algorithm]]<br />
* [http://maya:7575/ExpressionView/doc ActionScript source code documentation]<br />
* [[Media:Expressionview.xmldescription.pdf|XML file structure]]</div>Andreashttp://www2.unil.ch/cbg/index.php?title=ExpressionViewExpressionView2009-11-17T22:02:33Z<p>Andreas: </p>
<hr />
<div>[[image:Expressionview.screenshot.png|Screenshot of the ExpressionView applet|500px|left]]<br />
<br style="clear: both" /><br />
<br><br />
ExpressionView is an R package that provides an interactive environment to explore biclusters identified in gene expression data. A sophisticated ordering algorithm is used to present the biclusters in a visually appealing layout. From this overview, the user can select individual biclusters and access all the biologically relevant data associated with it. The package is aimed to facilitate the collaboration between bioinformaticians and life scientists who are not familiar with the R language.<br />
<br />
= Launch and download =<br />
<br />
== Launch the ExpressionView Flash applet == <br />
* [http://maya:7575/ExpressionView/bin/ExpressionView.html Launch ExpressionView]<br />
* [http://maya:7575/ExpressionView/bin/ExpressionView.html?filename=../data/ALL.small.evf Launch ExpressionView with ALL data (8 modules)]<br />
* [http://maya:7575/ExpressionView/bin/ExpressionView.html?filename=../data/ALL.large.evf Launch ExpressionView with ALL data (108 modules)]<br />
<br />
== Download the R package (includes the Flash applet)==<br />
<br />
== Download the stand-alone viewer (adobe AIR) ==<br />
If you prefer a stand-alone viewer, you can download and install the Adobe AIR build [http://maya:7575/ExpressionView/air/ExpressionView.air ExpressionView.air].<br><br />
To run the program, you need the AIR runtime environment which you can get from [http://get.adobe.com/air Adobe].<br><br />
ExpressionView creates files associations to .evf files, allowing you to simply double-click on such files in order to launch the viewer and load the data.<br />
<br />
== Download some sample data ==<br />
* [http://maya:7575/ExpressionView/bin/data/Expressionview.sampledata.all.small.evf Gene expression profile of adult T-cell acute lymphocytic leukemia (ALL) with 8 modules]<br />
* [http://maya:7575/ExpressionView/bin/Expressionview.sampledata.all.large.evf Gene expression profile of adult T-cell acute lymphocytic leukemia (ALL) with 108 modules]<br />
<br />
= Screenshots = <br />
<gallery widths="200px" heights="109px" perrow="3"><br />
image:Expressionview.screenshot.1.png|Startup screen<br />
image:Expressionview.screenshot.2.png|Global view after loading dataset<br />
image:Expressionview.screenshot.3.png|Highlighting modules<br />
image:Expressionview.screenshot.4.png|Zoom functions<br />
image:Expressionview.screenshot.5.png|Highlighting genes (probes) and samples<br />
image:Expressionview.screenshot.6.png|GO and KEGG associations<br />
image:Expressionview.screenshot.7.png|Modules view emphasizing the underlying gene expression data<br />
image:Expressionview.screenshot.8.png|Global view without gene expression data<br />
image:Expressionview.screenshot.9.png|Experiment description<br />
</gallery><br />
<br />
= Tutorials =<br />
There are several tutorials describing how to use ExpressionView:<br />
<br />
== R package ==<br />
<br />
== Flash applet ==<br />
<br />
= Additional documentation and downloads =<br />
* [[Media:Expressionview.ordering.pdf|Ordering algorithm]]<br />
* [http://maya:7575/ExpressionView/doc ActionScript source code documentation]<br />
* [[Media:Expressionview.xmldescription.pdf|XML file structure]]</div>Andreashttp://www2.unil.ch/cbg/index.php?title=ExpressionViewExpressionView2009-11-17T21:58:27Z<p>Andreas: </p>
<hr />
<div>[[image:Expressionview.screenshot.png|Screenshot of the ExpressionView applet|500px|left]]<br />
<br style="clear: both" /><br />
<br><br />
ExpressionView is an R package that provides an interactive environment to explore biclusters identified in gene expression data. A sophisticated ordering algorithm is used to present the biclusters in a visually appealing layout. From this overview, the user can select individual biclusters and access all the biologically relevant data associated with it. The package is aimed to facilitate the collaboration between bioinformaticians and life scientists who are not familiar with the R language.<br />
<br />
= Launch and download =<br />
<br />
== Launch the ExpressionView Flash applet == <br />
* [http://maya:7575/ExpressionView/bin/ExpressionView.html Launch ExpressionView]<br />
* [http://maya:7575/ExpressionView/bin/ExpressionView.html?filename=../data/ALL.small.evf Launch ExpressionView with ALL data (8 modules)]<br />
* [http://maya:7575/ExpressionView/bin/ExpressionView.html?filename=../data/ALL.large.evf Launch ExpressionView with ALL data (108 modules)]<br />
<br />
== Download the R package (includes the Flash applet)==<br />
<br />
== Download the stand-alone viewer (adobe AIR) ==<br />
If you prefer a stand-alone viewer, you can download and install the Adobe AIR build [http://maya:7575/ExpressionView/air/ExpressionView.air ExpressionView.air].<br><br />
To run the program, you need the AIR runtime environment which you can get from [http://get.adobe.com/air Adobe].<br />
ExpressionView creates files associations to .evf files, allowing you to simply double-click on such files in order to launch the viewer and load the file.<br />
<br />
== Download some sample data ==<br />
* [[Media:Expressionview.sampledata.all.small.evf|Gene expression profile of adult T-cell acute lymphocytic leukemia (ALL) with 8 modules]]<br />
* [[Media:Expressionview.sampledata.all.large.evf|Gene expression profile of adult T-cell acute lymphocytic leukemia (ALL) with 108 modules]]<br />
<br />
= Screenshots = <br />
<gallery widths="200px" heights="109px" perrow="3"><br />
image:Expressionview.screenshot.1.png|Startup screen<br />
image:Expressionview.screenshot.2.png|Global view after loading dataset<br />
image:Expressionview.screenshot.3.png|Highlighting modules<br />
image:Expressionview.screenshot.4.png|Zoom functions<br />
image:Expressionview.screenshot.5.png|Highlighting genes (probes) and samples<br />
image:Expressionview.screenshot.6.png|GO and KEGG associations<br />
image:Expressionview.screenshot.7.png|Modules view emphasizing the underlying gene expression data<br />
image:Expressionview.screenshot.8.png|Global view without gene expression data<br />
image:Expressionview.screenshot.9.png|Experiment description<br />
</gallery><br />
<br />
= Tutorials =<br />
There are several tutorials describing how to use ExpressionView:<br />
<br />
== R package ==<br />
<br />
== Flash applet ==<br />
<br />
= Additional documentation and downloads =<br />
* [[Media:Expressionview.ordering.pdf|Ordering algorithm]]<br />
* [http://maya:7575/ExpressionView/doc ActionScript source code documentation]<br />
* [[Media:Expressionview.xmldescription.pdf|XML file structure]]</div>Andreashttp://www2.unil.ch/cbg/index.php?title=ExpressionViewExpressionView2009-11-17T21:48:03Z<p>Andreas: </p>
<hr />
<div>[[image:Expressionview.screenshot.png|Screenshot of the ExpressionView applet|500px|left]]<br />
<br style="clear: both" /><br />
<br><br />
ExpressionView is an R package that provides an interactive environment to explore biclusters identified in gene expression data. A sophisticated ordering algorithm is used to present the biclusters in a visually appealing layout. From this overview, the user can select individual biclusters and access all the biologically relevant data associated with it. The package is aimed to facilitate the collaboration between bioinformaticians and life scientists who are not familiar with the R language.<br />
<br />
= Launch and download =<br />
<br />
== Launch the ExpressionView Flash applet == <br />
* [http://maya:7575/ExpressionView/bin/ExpressionView.html Launch ExpressionView]<br />
* [http://maya:7575/ExpressionView/bin/ExpressionView.html?filename=../data/ALL.small.xml Launch ExpressionView with ALL data (8 modules)]<br />
* [http://maya:7575/ExpressionView/bin/ExpressionView.html?filename=../data/ALL.large.xml Launch ExpressionView with ALL data (108 modules)]<br />
<br />
== Download the R package (includes the Flash applet)==<br />
<br />
== Download the stand-alone viewer (adobe AIR) ==<br />
If you prefer a stand-alone viewer, you can download and install the Adobe AIR build [http://maya:7575/ExpressionView/air/ExpressionView.air ExpressionView.air].<br><br />
To run the program, you need the AIR runtime environment, which you can get from [http://get.adobe.com/air Adobe].<br />
<br />
== Download some sample data ==<br />
* [[Media:Expressionview.sampledata.all.small.xml|Gene expression profile of adult T-cell acute lymphocytic leukemia (ALL) with 8 modules]]<br />
* [[Media:Expressionview.sampledata.all.large.xml|Gene expression profile of adult T-cell acute lymphocytic leukemia (ALL) with 108 modules]]<br />
<br />
= Screenshots = <br />
<gallery widths="200px" heights="109px" perrow="3"><br />
image:Expressionview.screenshot.1.png|Startup screen<br />
image:Expressionview.screenshot.2.png|Global view after loading dataset<br />
image:Expressionview.screenshot.3.png|Highlighting modules<br />
image:Expressionview.screenshot.4.png|Zoom functions<br />
image:Expressionview.screenshot.5.png|Highlighting genes (probes) and samples<br />
image:Expressionview.screenshot.6.png|GO and KEGG associations<br />
image:Expressionview.screenshot.7.png|Modules view emphasizing the underlying gene expression data<br />
image:Expressionview.screenshot.8.png|Global view without gene expression data<br />
image:Expressionview.screenshot.9.png|Experiment description<br />
</gallery><br />
<br />
= Tutorials =<br />
There are several tutorials describing how to use ExpressionView:<br />
<br />
== R package ==<br />
<br />
== Flash applet ==<br />
<br />
= Additional documentation and downloads =<br />
* [[Media:Expressionview.ordering.pdf|Ordering algorithm]]<br />
* [http://maya:7575/ExpressionView/doc ActionScript source code documentation]<br />
* [[Media:Expressionview.xmldescription.pdf|XML file structure]]</div>Andreashttp://www2.unil.ch/cbg/index.php?title=ExpressionViewExpressionView2009-11-17T21:42:26Z<p>Andreas: </p>
<hr />
<div>[[image:Expressionview.screenshot.png|Screenshot of the ExpressionView applet|500px|left]]<br />
<br style="clear: both" /><br />
<br><br />
ExpressionView is an R package that provides an interactive environment to explore biclusters identified in gene expression data. A sophisticated ordering algorithm is used to present the biclusters in a visually appealing layout. From this overview, the user can select individual biclusters and access all the biologically relevant data associated with it. The package is aimed to facilitate the collaboration between bioinformaticians and life scientists who are not familiar with the R language.<br />
<br />
= Launch and download =<br />
<br />
== Launch the ExpressionView Flash applet == <br />
* [http://maya:7575/ExpressionView/bin/ExpressionView.html Launch ExpressionView]<br />
* [http://maya:7575/ExpressionView/bin/ExpressionView.html?filename=../data/ALL.small.xml Launch ExpressionView with ALL data (8 modules)]<br />
* [http://maya:7575/ExpressionView/bin/ExpressionView.html?filename=../data/ALL.large.xml Launch ExpressionView with ALL data (108 modules)]<br />
<br />
== Download the R package (includes the Flash applet)==<br />
<br />
== Download the stand-alone viewer (adobe AIR) ==<br />
If you prefer a stand-alone viewer, you can download and install the Adobe AIR build of ExpressionView:<br />
[http://maya:7575/ExpressionView/air/ExpressionView.air ExpressionView.air]. Note that you first need to install the necessary runtime environment from [http://get.adobe.com/air].<br />
<br />
== Download some sample data ==<br />
* [[Media:Expressionview.sampledata.all.small.xml|Gene expression profile of adult T-cell acute lymphocytic leukemia (ALL) with 8 modules]]<br />
* [[Media:Expressionview.sampledata.all.large.xml|Gene expression profile of adult T-cell acute lymphocytic leukemia (ALL) with 108 modules]]<br />
<br />
= Screenshots = <br />
<gallery widths="200px" heights="109px" perrow="3"><br />
image:Expressionview.screenshot.1.png|Startup screen<br />
image:Expressionview.screenshot.2.png|Global view after loading dataset<br />
image:Expressionview.screenshot.3.png|Highlighting modules<br />
image:Expressionview.screenshot.4.png|Zoom functions<br />
image:Expressionview.screenshot.5.png|Highlighting genes (probes) and samples<br />
image:Expressionview.screenshot.6.png|GO and KEGG associations<br />
image:Expressionview.screenshot.7.png|Modules view emphasizing the underlying gene expression data<br />
image:Expressionview.screenshot.8.png|Global view without gene expression data<br />
image:Expressionview.screenshot.9.png|Experiment description<br />
</gallery><br />
<br />
= Tutorials =<br />
There are several tutorials describing how to use ExpressionView:<br />
<br />
== R package ==<br />
<br />
== Flash applet ==<br />
<br />
= Additional documentation and downloads =<br />
* [[Media:Expressionview.ordering.pdf|Ordering algorithm]]<br />
* [http://maya:7575/ExpressionView/doc ActionScript source code documentation]<br />
* [[Media:Expressionview.xmldescription.pdf|XML file structure]]</div>Andreashttp://www2.unil.ch/cbg/index.php?title=ExpressionViewExpressionView2009-11-16T12:01:23Z<p>Andreas: /* Launch and download */</p>
<hr />
<div>[[image:Expressionview.screenshot.png|Screenshot of the ExpressionView applet|500px|left]]<br />
<br style="clear: both" /><br />
<br><br />
ExpressionView is an R package that provides an interactive environment to explore biclusters identified in gene expression data. A sophisticated ordering algorithm is used to present the biclusters in a visually appealing layout that provides an intuitive summary of the results. From this overview, the user can select individual biclusters and access all the biologically relevant data associated with it. The package is aimed to facilitate the collaboration between bioinformaticians and life scientists who are not familiar with the R language.<br />
<br />
= Launch and download =<br />
<br />
== Launch the ExpressionView Flash applet == <br />
* [http://maya:7575/ExpressionView/bin/ExpressionView.html Launch ExpressionView]<br />
* [http://maya:7575/ExpressionView/bin/ExpressionView.html?filename=../data/ALL.small.xml Launch ExpressionView with ALL data (8 modules)]<br />
* [http://maya:7575/ExpressionView/bin/ExpressionView.html?filename=../data/ALL.large.xml Launch ExpressionView with ALL data (108 modules)]<br />
<br />
== Download the R package (includes the Flash applet)==<br />
<br />
== Download the standalone viewer (adobe AIR) ==<br />
== Download some sample data ==<br />
* [[Media:Expressionview.sampledata.all.small.xml|Gene expression profile of adult T-cell acute lymphocytic leukemia (ALL) with 8 modules]]<br />
* [[Media:Expressionview.sampledata.all.large.xml|Gene expression profile of adult T-cell acute lymphocytic leukemia (ALL) with 108 modules]]<br />
<br />
= Screenshots = <br />
<gallery widths="200px" heights="109px" perrow="3"><br />
image:Expressionview.screenshot.1.png|Startup screen<br />
image:Expressionview.screenshot.2.png|Global view after loading dataset<br />
image:Expressionview.screenshot.3.png|Highlighting modules<br />
image:Expressionview.screenshot.4.png|Zoom functions<br />
image:Expressionview.screenshot.5.png|Highlighting genes (probes) and samples<br />
image:Expressionview.screenshot.6.png|GO and KEGG associations<br />
image:Expressionview.screenshot.7.png|Modules view emphasizing the underlying gene expression data<br />
image:Expressionview.screenshot.8.png|Global view without gene expression data<br />
image:Expressionview.screenshot.9.png|Experiment description<br />
</gallery><br />
<br />
= Tutorials =<br />
There are several tutorials describing how to use ExpressionView:<br />
<br />
== R package ==<br />
<br />
== Flash applet ==<br />
<br />
= Additional documentation and downloads =<br />
* [[Media:Expressionview.ordering.pdf|Ordering algorithm]]<br />
* [http://maya:7575/ExpressionView/doc ActionScript source code documentation]<br />
* [[Media:Expressionview.xmldescription.pdf|XML file structure]]</div>Andreashttp://www2.unil.ch/cbg/index.php?title=ExpressionViewExpressionView2009-11-16T11:46:17Z<p>Andreas: </p>
<hr />
<div>[[image:Expressionview.screenshot.png|Screenshot of the ExpressionView applet|500px|left]]<br />
<br style="clear: both" /><br />
<br><br />
ExpressionView is an R package that provides an interactive environment to explore biclusters identified in gene expression data. A sophisticated ordering algorithm is used to present the biclusters in a visually appealing layout that provides an intuitive summary of the results. From this overview, the user can select individual biclusters and access all the biologically relevant data associated with it. The package is aimed to facilitate the collaboration between bioinformaticians and life scientists who are not familiar with the R language.<br />
<br />
= Launch and download =<br />
<br />
== Launch the ExpressionView Flash applet<br />
* [http://maya:7575/ExpressionView/bin/ExpressionView.html Launch ExpressionView]<br />
* [http://maya:7575/ExpressionView/bin/ExpressionView.html?filename=../data/ALL.small.xml Launch ExpressionView with ALL data (8 modules)]<br />
* [http://maya:7575/ExpressionView/bin/ExpressionView.html?filename=../data/ALL.large.xml Launch ExpressionView with ALL data (108 modules)]<br />
<br />
== Download the R package (includes the Flash applet)==<br />
<br />
== Download the standalone viewer (adobe AIR) ==<br />
== Download some sample data ==<br />
* [[Media:Expressionview.sampledata.all.small.xml|Gene expression profile of adult T-cell acute lymphocytic leukemia (ALL) with 8 modules]]<br />
* [[Media:Expressionview.sampledata.all.large.xml|Gene expression profile of adult T-cell acute lymphocytic leukemia (ALL) with 108 modules]]<br />
<br />
<br />
<br />
= Screenshots = <br />
<gallery widths="200px" heights="109px" perrow="3"><br />
image:Expressionview.screenshot.1.png|Startup screen<br />
image:Expressionview.screenshot.2.png|Global view after loading dataset<br />
image:Expressionview.screenshot.3.png|Highlighting modules<br />
image:Expressionview.screenshot.4.png|Zoom functions<br />
image:Expressionview.screenshot.5.png|Highlighting genes (probes) and samples<br />
image:Expressionview.screenshot.6.png|GO and KEGG associations<br />
image:Expressionview.screenshot.7.png|Modules view emphasizing the underlying gene expression data<br />
image:Expressionview.screenshot.8.png|Global view without gene expression data<br />
image:Expressionview.screenshot.9.png|Experiment description<br />
</gallery><br />
<br />
= Tutorials =<br />
There are several tutorials describing how to use ExpressionView:<br />
<br />
== R package ==<br />
<br />
== Flash applet ==<br />
<br />
= Additional documentation and downloads =<br />
* [[Media:Expressionview.ordering.pdf|Ordering algorithm]]<br />
* [http://maya:7575/ExpressionView/doc ActionScript source code documentation]<br />
* [[Media:Expressionview.xmldescription.pdf|XML file structure]]</div>Andreashttp://www2.unil.ch/cbg/index.php?title=ExpressionViewExpressionView2009-11-16T10:58:59Z<p>Andreas: </p>
<hr />
<div>[[image:Expressionview.screenshot.png|Screenshot of the ExpressionView applet|500px|left]]<br />
<br style="clear: both" /><br />
<br><br />
ExpressionView is an R package that provides an interactive environment to explore biclusters identified in gene expression data. A sophisticated ordering algorithm is used to present the biclusters in a visually appealing layout that provides an intuitive summary of the results. From this overview, the user can select individual biclusters and access all the biologically relevant data associated with it. The package is aimed to facilitate the collaboration between bioinformaticians and life scientists who are not familiar with the R language.<br />
<br />
= Launch =<br />
* [http://maya:7575/ExpressionView/bin/ExpressionView.html Launch ExpressionView]<br />
* [http://maya:7575/ExpressionView/bin/ExpressionView.html?filename=../data/ALL.small.xml Launch ExpressionView with ALL data (8 modules)]<br />
* [http://maya:7575/ExpressionView/bin/ExpressionView.html?filename=../data/ALL.large.xml Launch ExpressionView with ALL data (108 modules)]<br />
<br />
= Screenshots = <br />
<gallery widths="200px" heights="109px" perrow="3"><br />
image:Expressionview.screenshot.1.png|Startup screen<br />
image:Expressionview.screenshot.2.png|Global view after loading dataset<br />
image:Expressionview.screenshot.3.png|Highlighting modules<br />
image:Expressionview.screenshot.4.png|Zoom functions<br />
image:Expressionview.screenshot.5.png|Highlighting genes (probes) and samples<br />
image:Expressionview.screenshot.6.png|GO and KEGG associations<br />
image:Expressionview.screenshot.7.png|Modules view emphasizing the underlying gene expression data<br />
image:Expressionview.screenshot.8.png|Global view without gene expression data<br />
image:Expressionview.screenshot.9.png|Experiment description<br />
</gallery><br />
<br />
= Download =<br />
== R package ==<br />
== Standalone version of the viewer (adobe AIR) ==<br />
== Sample data ==<br />
* [[Media:Expressionview.sampledata.all.small.xml|Gene expression profile of adult T-cell acute lymphocytic leukemia (ALL) with 8 modules]]<br />
* [[Media:Expressionview.sampledata.all.large.xml|Gene expression profile of adult T-cell acute lymphocytic leukemia (ALL) with 108 modules]]<br />
<br />
= Tutorials =<br />
There are several tutorials describing how to use ExpressionView:<br />
<br />
== R package ==<br />
<br />
== Flash applet ==<br />
<br />
= Additional documentation and downloads =<br />
* [[Media:Expressionview.ordering.pdf|Ordering algorithm]]<br />
* [http://maya:7575/ExpressionView/doc ActionScript source code documentation]<br />
* [[Media:Expressionview.xmldescription.pdf|XML file structure]]</div>Andreashttp://www2.unil.ch/cbg/index.php?title=ExpressionViewExpressionView2009-11-16T10:55:36Z<p>Andreas: </p>
<hr />
<div>[[image:Expressionview.screenshot.png|Screenshot of the ExpressionView applet|500px|left]]<br><br />
<br />
ExpressionView is an R package that provides an interactive environment to explore biclusters identified in gene expression data. A sophisticated ordering algorithm is used to present the biclusters in a visually appealing layout that provides an intuitive summary of the results. From this overview, the user can select individual biclusters and access all the biologically relevant data associated with it. The package is aimed to facilitate the collaboration between bioinformaticians and life scientists who are not familiar with the R language.<br />
<br />
= Launch =<br />
* [http://maya:7575/ExpressionView/bin/ExpressionView.html Launch ExpressionView]<br />
* [http://maya:7575/ExpressionView/bin/ExpressionView.html?filename=../data/ALL.small.xml Launch ExpressionView with ALL data (8 modules)]<br />
* [http://maya:7575/ExpressionView/bin/ExpressionView.html?filename=../data/ALL.large.xml Launch ExpressionView with ALL data (108 modules)]<br />
<br />
= Screenshots = <br />
<gallery widths="200px" heights="109px" perrow="3"><br />
image:Expressionview.screenshot.1.png|Startup screen<br />
image:Expressionview.screenshot.2.png|Global view after loading dataset<br />
image:Expressionview.screenshot.3.png|Highlighting modules<br />
image:Expressionview.screenshot.4.png|Zoom functions<br />
image:Expressionview.screenshot.5.png|Highlighting genes (probes) and samples<br />
image:Expressionview.screenshot.6.png|GO and KEGG associations<br />
image:Expressionview.screenshot.7.png|Modules view emphasizing the underlying gene expression data<br />
image:Expressionview.screenshot.8.png|Global view without gene expression data<br />
image:Expressionview.screenshot.9.png|Experiment description<br />
</gallery><br />
<br />
= Download =<br />
== R package ==<br />
== Standalone version of the viewer (adobe AIR) ==<br />
== Sample data ==<br />
* [[Media:Expressionview.sampledata.all.small.xml|Gene expression profile of adult T-cell acute lymphocytic leukemia (ALL) with 8 modules]]<br />
* [[Media:Expressionview.sampledata.all.large.xml|Gene expression profile of adult T-cell acute lymphocytic leukemia (ALL) with 108 modules]]<br />
<br />
= Tutorials =<br />
There are several tutorials describing how to use ExpressionView:<br />
<br />
== R package ==<br />
<br />
== Flash applet ==<br />
<br />
= Additional documentation and downloads =<br />
* [[Media:Expressionview.ordering.pdf|Ordering algorithm]]<br />
* [http://maya:7575/ExpressionView/doc ActionScript source code documentation]<br />
* [[Media:Expressionview.xmldescription.pdf|XML file structure]]</div>Andreashttp://www2.unil.ch/cbg/index.php?title=ExpressionViewExpressionView2009-11-16T10:51:42Z<p>Andreas: /* Download */</p>
<hr />
<div>[[image:Expressionview.screenshot.png|Screenshot of the ExpressionView applet|300px|right]]<br />
<br />
ExpressionView is an R package that provides an interactive environment to explore biclusters identified in gene expression data. A sophisticated ordering algorithm is used to present the biclusters in a visually appealing layout that provides an intuitive summary of the results. From this overview, the user can select individual biclusters and access all the biologically relevant data associated with it. The package is aimed to facilitate the collaboration between bioinformaticians and life scientists who are not familiar with the R language.<br />
<br />
= Launch =<br />
* [http://maya:7575/ExpressionView/bin/ExpressionView.html Launch ExpressionView]<br />
* [http://maya:7575/ExpressionView/bin/ExpressionView.html?filename=../data/ALL.small.xml Launch ExpressionView with ALL data (8 modules)]<br />
* [http://maya:7575/ExpressionView/bin/ExpressionView.html?filename=../data/ALL.large.xml Launch ExpressionView with ALL data (108 modules)]<br />
<br />
= Screenshots = <br />
<gallery widths="200px" heights="109px" perrow="3"><br />
image:Expressionview.screenshot.1.png|Startup screen<br />
image:Expressionview.screenshot.2.png|Global view after loading dataset<br />
image:Expressionview.screenshot.3.png|Highlighting modules<br />
image:Expressionview.screenshot.4.png|Zoom functions<br />
image:Expressionview.screenshot.5.png|Highlighting genes (probes) and samples<br />
image:Expressionview.screenshot.6.png|GO and KEGG associations<br />
image:Expressionview.screenshot.7.png|Modules view emphasizing the underlying gene expression data<br />
image:Expressionview.screenshot.8.png|Global view without gene expression data<br />
image:Expressionview.screenshot.9.png|Experiment description<br />
</gallery><br />
<br />
= Download =<br />
== R package ==<br />
== Standalone version of the viewer (adobe AIR) ==<br />
== Sample data ==<br />
* [[Media:Expressionview.sampledata.all.small.xml|Gene expression profile of adult T-cell acute lymphocytic leukemia (ALL) with 8 modules]]<br />
* [[Media:Expressionview.sampledata.all.large.xml|Gene expression profile of adult T-cell acute lymphocytic leukemia (ALL) with 108 modules]]<br />
<br />
= Tutorials =<br />
There are several tutorials describing how to use ExpressionView:<br />
<br />
== R package ==<br />
<br />
== Flash applet ==<br />
<br />
= Additional documentation and downloads =<br />
* [[Media:Expressionview.ordering.pdf|Ordering algorithm]]<br />
* [http://maya:7575/ExpressionView/doc ActionScript source code documentation]<br />
* [[Media:Expressionview.xmldescription.pdf|XML file structure]]</div>Andreashttp://www2.unil.ch/cbg/index.php?title=ExpressionViewExpressionView2009-11-16T09:50:23Z<p>Andreas: /* Additional documentation and downloads */</p>
<hr />
<div>[[image:Expressionview.screenshot.png|Screenshot of the ExpressionView applet|300px|right]]<br />
<br />
ExpressionView is an R package that provides an interactive environment to explore biclusters identified in gene expression data. A sophisticated ordering algorithm is used to present the biclusters in a visually appealing layout that provides an intuitive summary of the results. From this overview, the user can select individual biclusters and access all the biologically relevant data associated with it. The package is aimed to facilitate the collaboration between bioinformaticians and life scientists who are not familiar with the R language.<br />
<br />
= Launch =<br />
* [http://maya:7575/ExpressionView/bin/ExpressionView.html Launch ExpressionView]<br />
* [http://maya:7575/ExpressionView/bin/ExpressionView.html?filename=../data/ALL.small.xml Launch ExpressionView with ALL data (8 modules)]<br />
* [http://maya:7575/ExpressionView/bin/ExpressionView.html?filename=../data/ALL.large.xml Launch ExpressionView with ALL data (108 modules)]<br />
<br />
= Screenshots = <br />
<gallery widths="200px" heights="109px" perrow="3"><br />
image:Expressionview.screenshot.1.png|Startup screen<br />
image:Expressionview.screenshot.2.png|Global view after loading dataset<br />
image:Expressionview.screenshot.3.png|Highlighting modules<br />
image:Expressionview.screenshot.4.png|Zoom functions<br />
image:Expressionview.screenshot.5.png|Highlighting genes (probes) and samples<br />
image:Expressionview.screenshot.6.png|GO and KEGG associations<br />
image:Expressionview.screenshot.7.png|Modules view emphasizing the underlying gene expression data<br />
image:Expressionview.screenshot.8.png|Global view without gene expression data<br />
image:Expressionview.screenshot.9.png|Experiment description<br />
</gallery><br />
<br />
= Download =<br />
<br />
<br />
= Tutorials =<br />
There are several tutorials describing how to use ExpressionView:<br />
<br />
== R package ==<br />
<br />
== Flash applet ==<br />
<br />
= Additional documentation and downloads =<br />
* [[Media:Expressionview.ordering.pdf|Ordering algorithm]]<br />
* [http://maya:7575/ExpressionView/doc ActionScript source code documentation]<br />
* [[Media:Expressionview.xmldescription.pdf|XML file structure]]</div>Andreashttp://www2.unil.ch/cbg/index.php?title=ExpressionViewExpressionView2009-11-16T09:49:50Z<p>Andreas: /* Additional documentation and downloads */</p>
<hr />
<div>[[image:Expressionview.screenshot.png|Screenshot of the ExpressionView applet|300px|right]]<br />
<br />
ExpressionView is an R package that provides an interactive environment to explore biclusters identified in gene expression data. A sophisticated ordering algorithm is used to present the biclusters in a visually appealing layout that provides an intuitive summary of the results. From this overview, the user can select individual biclusters and access all the biologically relevant data associated with it. The package is aimed to facilitate the collaboration between bioinformaticians and life scientists who are not familiar with the R language.<br />
<br />
= Launch =<br />
* [http://maya:7575/ExpressionView/bin/ExpressionView.html Launch ExpressionView]<br />
* [http://maya:7575/ExpressionView/bin/ExpressionView.html?filename=../data/ALL.small.xml Launch ExpressionView with ALL data (8 modules)]<br />
* [http://maya:7575/ExpressionView/bin/ExpressionView.html?filename=../data/ALL.large.xml Launch ExpressionView with ALL data (108 modules)]<br />
<br />
= Screenshots = <br />
<gallery widths="200px" heights="109px" perrow="3"><br />
image:Expressionview.screenshot.1.png|Startup screen<br />
image:Expressionview.screenshot.2.png|Global view after loading dataset<br />
image:Expressionview.screenshot.3.png|Highlighting modules<br />
image:Expressionview.screenshot.4.png|Zoom functions<br />
image:Expressionview.screenshot.5.png|Highlighting genes (probes) and samples<br />
image:Expressionview.screenshot.6.png|GO and KEGG associations<br />
image:Expressionview.screenshot.7.png|Modules view emphasizing the underlying gene expression data<br />
image:Expressionview.screenshot.8.png|Global view without gene expression data<br />
image:Expressionview.screenshot.9.png|Experiment description<br />
</gallery><br />
<br />
= Download =<br />
<br />
<br />
= Tutorials =<br />
There are several tutorials describing how to use ExpressionView:<br />
<br />
== R package ==<br />
<br />
== Flash applet ==<br />
<br />
= Additional documentation and downloads =<br />
* [[Media:Expressionview.ordering.pdf|Ordering algorithm]]<br />
* [http://maya:7575/ExpressionView/doc ActionScript source code documentation]<br />
* [[Media:Expressionview.xml.pdf|XML file structure]]</div>Andreashttp://www2.unil.ch/cbg/index.php?title=File:Expressionview.xmldescription.pdfFile:Expressionview.xmldescription.pdf2009-11-16T09:48:37Z<p>Andreas: Documentation of the ExpressionView XML file structure.</p>
<hr />
<div>Documentation of the ExpressionView XML file structure.</div>Andreashttp://www2.unil.ch/cbg/index.php?title=ExpressionViewExpressionView2009-11-16T09:45:08Z<p>Andreas: /* Additional documentation */</p>
<hr />
<div>[[image:Expressionview.screenshot.png|Screenshot of the ExpressionView applet|300px|right]]<br />
<br />
ExpressionView is an R package that provides an interactive environment to explore biclusters identified in gene expression data. A sophisticated ordering algorithm is used to present the biclusters in a visually appealing layout that provides an intuitive summary of the results. From this overview, the user can select individual biclusters and access all the biologically relevant data associated with it. The package is aimed to facilitate the collaboration between bioinformaticians and life scientists who are not familiar with the R language.<br />
<br />
= Launch =<br />
* [http://maya:7575/ExpressionView/bin/ExpressionView.html Launch ExpressionView]<br />
* [http://maya:7575/ExpressionView/bin/ExpressionView.html?filename=../data/ALL.small.xml Launch ExpressionView with ALL data (8 modules)]<br />
* [http://maya:7575/ExpressionView/bin/ExpressionView.html?filename=../data/ALL.large.xml Launch ExpressionView with ALL data (108 modules)]<br />
<br />
= Screenshots = <br />
<gallery widths="200px" heights="109px" perrow="3"><br />
image:Expressionview.screenshot.1.png|Startup screen<br />
image:Expressionview.screenshot.2.png|Global view after loading dataset<br />
image:Expressionview.screenshot.3.png|Highlighting modules<br />
image:Expressionview.screenshot.4.png|Zoom functions<br />
image:Expressionview.screenshot.5.png|Highlighting genes (probes) and samples<br />
image:Expressionview.screenshot.6.png|GO and KEGG associations<br />
image:Expressionview.screenshot.7.png|Modules view emphasizing the underlying gene expression data<br />
image:Expressionview.screenshot.8.png|Global view without gene expression data<br />
image:Expressionview.screenshot.9.png|Experiment description<br />
</gallery><br />
<br />
= Download =<br />
<br />
<br />
= Tutorials =<br />
There are several tutorials describing how to use ExpressionView:<br />
<br />
== R package ==<br />
<br />
== Flash applet ==<br />
<br />
= Additional documentation and downloads =<br />
* [[Media:Expressionview.ordering.pdf|Ordering algorithm]]<br />
* [http://maya:7575/ExpressionView/doc ActionScript source code documentation]<br />
* [[Media:Expressionview-xml|XML file structure]]</div>Andreashttp://www2.unil.ch/cbg/index.php?title=ExpressionViewExpressionView2009-11-16T09:44:28Z<p>Andreas: /* Additional documentation */</p>
<hr />
<div>[[image:Expressionview.screenshot.png|Screenshot of the ExpressionView applet|300px|right]]<br />
<br />
ExpressionView is an R package that provides an interactive environment to explore biclusters identified in gene expression data. A sophisticated ordering algorithm is used to present the biclusters in a visually appealing layout that provides an intuitive summary of the results. From this overview, the user can select individual biclusters and access all the biologically relevant data associated with it. The package is aimed to facilitate the collaboration between bioinformaticians and life scientists who are not familiar with the R language.<br />
<br />
= Launch =<br />
* [http://maya:7575/ExpressionView/bin/ExpressionView.html Launch ExpressionView]<br />
* [http://maya:7575/ExpressionView/bin/ExpressionView.html?filename=../data/ALL.small.xml Launch ExpressionView with ALL data (8 modules)]<br />
* [http://maya:7575/ExpressionView/bin/ExpressionView.html?filename=../data/ALL.large.xml Launch ExpressionView with ALL data (108 modules)]<br />
<br />
= Screenshots = <br />
<gallery widths="200px" heights="109px" perrow="3"><br />
image:Expressionview.screenshot.1.png|Startup screen<br />
image:Expressionview.screenshot.2.png|Global view after loading dataset<br />
image:Expressionview.screenshot.3.png|Highlighting modules<br />
image:Expressionview.screenshot.4.png|Zoom functions<br />
image:Expressionview.screenshot.5.png|Highlighting genes (probes) and samples<br />
image:Expressionview.screenshot.6.png|GO and KEGG associations<br />
image:Expressionview.screenshot.7.png|Modules view emphasizing the underlying gene expression data<br />
image:Expressionview.screenshot.8.png|Global view without gene expression data<br />
image:Expressionview.screenshot.9.png|Experiment description<br />
</gallery><br />
<br />
= Download =<br />
<br />
<br />
= Tutorials =<br />
There are several tutorials describing how to use ExpressionView:<br />
<br />
== R package ==<br />
<br />
== Flash applet ==<br />
<br />
= Additional documentation =<br />
* [[Media:Expressionview.ordering.pdf|Ordering algorithm]]<br />
* [http://maya:7575/ExpressionView/doc ActionScript source code documentation]<br />
* [[Media:Expressionview-xml|XML file structure]]</div>Andreashttp://www2.unil.ch/cbg/index.php?title=ExpressionViewExpressionView2009-11-16T09:44:07Z<p>Andreas: /* Additional documentation */</p>
<hr />
<div>[[image:Expressionview.screenshot.png|Screenshot of the ExpressionView applet|300px|right]]<br />
<br />
ExpressionView is an R package that provides an interactive environment to explore biclusters identified in gene expression data. A sophisticated ordering algorithm is used to present the biclusters in a visually appealing layout that provides an intuitive summary of the results. From this overview, the user can select individual biclusters and access all the biologically relevant data associated with it. The package is aimed to facilitate the collaboration between bioinformaticians and life scientists who are not familiar with the R language.<br />
<br />
= Launch =<br />
* [http://maya:7575/ExpressionView/bin/ExpressionView.html Launch ExpressionView]<br />
* [http://maya:7575/ExpressionView/bin/ExpressionView.html?filename=../data/ALL.small.xml Launch ExpressionView with ALL data (8 modules)]<br />
* [http://maya:7575/ExpressionView/bin/ExpressionView.html?filename=../data/ALL.large.xml Launch ExpressionView with ALL data (108 modules)]<br />
<br />
= Screenshots = <br />
<gallery widths="200px" heights="109px" perrow="3"><br />
image:Expressionview.screenshot.1.png|Startup screen<br />
image:Expressionview.screenshot.2.png|Global view after loading dataset<br />
image:Expressionview.screenshot.3.png|Highlighting modules<br />
image:Expressionview.screenshot.4.png|Zoom functions<br />
image:Expressionview.screenshot.5.png|Highlighting genes (probes) and samples<br />
image:Expressionview.screenshot.6.png|GO and KEGG associations<br />
image:Expressionview.screenshot.7.png|Modules view emphasizing the underlying gene expression data<br />
image:Expressionview.screenshot.8.png|Global view without gene expression data<br />
image:Expressionview.screenshot.9.png|Experiment description<br />
</gallery><br />
<br />
= Download =<br />
<br />
<br />
= Tutorials =<br />
There are several tutorials describing how to use ExpressionView:<br />
<br />
== R package ==<br />
<br />
== Flash applet ==<br />
<br />
= Additional documentation =<br />
* [[Media:Expressionview.ordering.pdf|Ordering algorithm]]<br />
* {{Pdf|Expressionview.ordering.pdf|Ordering algorithm}}<br />
* [http://maya:7575/ExpressionView/doc ActionScript source code documentation]<br />
* [[Media:Expressionview-xml|XML file structure]]</div>Andreashttp://www2.unil.ch/cbg/index.php?title=ExpressionViewExpressionView2009-11-16T09:38:11Z<p>Andreas: /* Additional documentation */</p>
<hr />
<div>[[image:Expressionview.screenshot.png|Screenshot of the ExpressionView applet|300px|right]]<br />
<br />
ExpressionView is an R package that provides an interactive environment to explore biclusters identified in gene expression data. A sophisticated ordering algorithm is used to present the biclusters in a visually appealing layout that provides an intuitive summary of the results. From this overview, the user can select individual biclusters and access all the biologically relevant data associated with it. The package is aimed to facilitate the collaboration between bioinformaticians and life scientists who are not familiar with the R language.<br />
<br />
= Launch =<br />
* [http://maya:7575/ExpressionView/bin/ExpressionView.html Launch ExpressionView]<br />
* [http://maya:7575/ExpressionView/bin/ExpressionView.html?filename=../data/ALL.small.xml Launch ExpressionView with ALL data (8 modules)]<br />
* [http://maya:7575/ExpressionView/bin/ExpressionView.html?filename=../data/ALL.large.xml Launch ExpressionView with ALL data (108 modules)]<br />
<br />
= Screenshots = <br />
<gallery widths="200px" heights="109px" perrow="3"><br />
image:Expressionview.screenshot.1.png|Startup screen<br />
image:Expressionview.screenshot.2.png|Global view after loading dataset<br />
image:Expressionview.screenshot.3.png|Highlighting modules<br />
image:Expressionview.screenshot.4.png|Zoom functions<br />
image:Expressionview.screenshot.5.png|Highlighting genes (probes) and samples<br />
image:Expressionview.screenshot.6.png|GO and KEGG associations<br />
image:Expressionview.screenshot.7.png|Modules view emphasizing the underlying gene expression data<br />
image:Expressionview.screenshot.8.png|Global view without gene expression data<br />
image:Expressionview.screenshot.9.png|Experiment description<br />
</gallery><br />
<br />
= Download =<br />
<br />
<br />
= Tutorials =<br />
There are several tutorials describing how to use ExpressionView:<br />
<br />
== R package ==<br />
<br />
== Flash applet ==<br />
<br />
= Additional documentation =<br />
* [[Media:Expressionview.ordering|Ordering algorithm]]<br />
* [http://maya:7575/ExpressionView/doc ActionScript source code documentation]<br />
* [[Media:Expressionview-xml|XML file structure]]</div>Andreashttp://www2.unil.ch/cbg/index.php?title=ExpressionViewExpressionView2009-11-16T09:36:11Z<p>Andreas: /* Additional documentation */</p>
<hr />
<div>[[image:Expressionview.screenshot.png|Screenshot of the ExpressionView applet|300px|right]]<br />
<br />
ExpressionView is an R package that provides an interactive environment to explore biclusters identified in gene expression data. A sophisticated ordering algorithm is used to present the biclusters in a visually appealing layout that provides an intuitive summary of the results. From this overview, the user can select individual biclusters and access all the biologically relevant data associated with it. The package is aimed to facilitate the collaboration between bioinformaticians and life scientists who are not familiar with the R language.<br />
<br />
= Launch =<br />
* [http://maya:7575/ExpressionView/bin/ExpressionView.html Launch ExpressionView]<br />
* [http://maya:7575/ExpressionView/bin/ExpressionView.html?filename=../data/ALL.small.xml Launch ExpressionView with ALL data (8 modules)]<br />
* [http://maya:7575/ExpressionView/bin/ExpressionView.html?filename=../data/ALL.large.xml Launch ExpressionView with ALL data (108 modules)]<br />
<br />
= Screenshots = <br />
<gallery widths="200px" heights="109px" perrow="3"><br />
image:Expressionview.screenshot.1.png|Startup screen<br />
image:Expressionview.screenshot.2.png|Global view after loading dataset<br />
image:Expressionview.screenshot.3.png|Highlighting modules<br />
image:Expressionview.screenshot.4.png|Zoom functions<br />
image:Expressionview.screenshot.5.png|Highlighting genes (probes) and samples<br />
image:Expressionview.screenshot.6.png|GO and KEGG associations<br />
image:Expressionview.screenshot.7.png|Modules view emphasizing the underlying gene expression data<br />
image:Expressionview.screenshot.8.png|Global view without gene expression data<br />
image:Expressionview.screenshot.9.png|Experiment description<br />
</gallery><br />
<br />
= Download =<br />
<br />
<br />
= Tutorials =<br />
There are several tutorials describing how to use ExpressionView:<br />
<br />
== R package ==<br />
<br />
== Flash applet ==<br />
<br />
= Additional documentation =<br />
* [[pdf:Expressionview.ordering|Ordering algorithm]]<br />
* [http://maya:7575/ExpressionView/doc ActionScript source code documentation]<br />
* [[pdf:Expressionview-xml|XML file structure]]</div>Andreashttp://www2.unil.ch/cbg/index.php?title=ExpressionViewExpressionView2009-11-16T09:35:24Z<p>Andreas: /* Additional documentation */</p>
<hr />
<div>[[image:Expressionview.screenshot.png|Screenshot of the ExpressionView applet|300px|right]]<br />
<br />
ExpressionView is an R package that provides an interactive environment to explore biclusters identified in gene expression data. A sophisticated ordering algorithm is used to present the biclusters in a visually appealing layout that provides an intuitive summary of the results. From this overview, the user can select individual biclusters and access all the biologically relevant data associated with it. The package is aimed to facilitate the collaboration between bioinformaticians and life scientists who are not familiar with the R language.<br />
<br />
= Launch =<br />
* [http://maya:7575/ExpressionView/bin/ExpressionView.html Launch ExpressionView]<br />
* [http://maya:7575/ExpressionView/bin/ExpressionView.html?filename=../data/ALL.small.xml Launch ExpressionView with ALL data (8 modules)]<br />
* [http://maya:7575/ExpressionView/bin/ExpressionView.html?filename=../data/ALL.large.xml Launch ExpressionView with ALL data (108 modules)]<br />
<br />
= Screenshots = <br />
<gallery widths="200px" heights="109px" perrow="3"><br />
image:Expressionview.screenshot.1.png|Startup screen<br />
image:Expressionview.screenshot.2.png|Global view after loading dataset<br />
image:Expressionview.screenshot.3.png|Highlighting modules<br />
image:Expressionview.screenshot.4.png|Zoom functions<br />
image:Expressionview.screenshot.5.png|Highlighting genes (probes) and samples<br />
image:Expressionview.screenshot.6.png|GO and KEGG associations<br />
image:Expressionview.screenshot.7.png|Modules view emphasizing the underlying gene expression data<br />
image:Expressionview.screenshot.8.png|Global view without gene expression data<br />
image:Expressionview.screenshot.9.png|Experiment description<br />
</gallery><br />
<br />
= Download =<br />
<br />
<br />
= Tutorials =<br />
There are several tutorials describing how to use ExpressionView:<br />
<br />
== R package ==<br />
<br />
== Flash applet ==<br />
<br />
= Additional documentation =<br />
* [[pdf:Expressionview.ordering.pdf|Ordering algorithm]]<br />
* [http://maya:7575/ExpressionView/doc ActionScript source code documentation]<br />
* [[pdf:Expressionview-xml|XML file structure]]</div>Andreashttp://www2.unil.ch/cbg/index.php?title=ExpressionViewExpressionView2009-11-16T09:34:26Z<p>Andreas: /* Additional documentation */</p>
<hr />
<div>[[image:Expressionview.screenshot.png|Screenshot of the ExpressionView applet|300px|right]]<br />
<br />
ExpressionView is an R package that provides an interactive environment to explore biclusters identified in gene expression data. A sophisticated ordering algorithm is used to present the biclusters in a visually appealing layout that provides an intuitive summary of the results. From this overview, the user can select individual biclusters and access all the biologically relevant data associated with it. The package is aimed to facilitate the collaboration between bioinformaticians and life scientists who are not familiar with the R language.<br />
<br />
= Launch =<br />
* [http://maya:7575/ExpressionView/bin/ExpressionView.html Launch ExpressionView]<br />
* [http://maya:7575/ExpressionView/bin/ExpressionView.html?filename=../data/ALL.small.xml Launch ExpressionView with ALL data (8 modules)]<br />
* [http://maya:7575/ExpressionView/bin/ExpressionView.html?filename=../data/ALL.large.xml Launch ExpressionView with ALL data (108 modules)]<br />
<br />
= Screenshots = <br />
<gallery widths="200px" heights="109px" perrow="3"><br />
image:Expressionview.screenshot.1.png|Startup screen<br />
image:Expressionview.screenshot.2.png|Global view after loading dataset<br />
image:Expressionview.screenshot.3.png|Highlighting modules<br />
image:Expressionview.screenshot.4.png|Zoom functions<br />
image:Expressionview.screenshot.5.png|Highlighting genes (probes) and samples<br />
image:Expressionview.screenshot.6.png|GO and KEGG associations<br />
image:Expressionview.screenshot.7.png|Modules view emphasizing the underlying gene expression data<br />
image:Expressionview.screenshot.8.png|Global view without gene expression data<br />
image:Expressionview.screenshot.9.png|Experiment description<br />
</gallery><br />
<br />
= Download =<br />
<br />
<br />
= Tutorials =<br />
There are several tutorials describing how to use ExpressionView:<br />
<br />
== R package ==<br />
<br />
== Flash applet ==<br />
<br />
= Additional documentation =<br />
* [[pdf:Expressionview.ordering|Ordering algorithm]]<br />
* [http://maya:7575/ExpressionView/doc ActionScript source code documentation]<br />
* [[pdf:Expressionview-xml|XML file structure]]</div>Andreashttp://www2.unil.ch/cbg/index.php?title=File:Expressionview.ordering.pdfFile:Expressionview.ordering.pdf2009-11-16T09:33:52Z<p>Andreas: </p>
<hr />
<div></div>Andreashttp://www2.unil.ch/cbg/index.php?title=ExpressionViewExpressionView2009-11-16T08:26:56Z<p>Andreas: /* Additional documentation */</p>
<hr />
<div>[[image:Expressionview.screenshot.png|Screenshot of the ExpressionView applet|300px|right]]<br />
<br />
ExpressionView is an R package that provides an interactive environment to explore biclusters identified in gene expression data. A sophisticated ordering algorithm is used to present the biclusters in a visually appealing layout that provides an intuitive summary of the results. From this overview, the user can select individual biclusters and access all the biologically relevant data associated with it. The package is aimed to facilitate the collaboration between bioinformaticians and life scientists who are not familiar with the R language.<br />
<br />
= Launch =<br />
* [http://maya:7575/ExpressionView/bin/ExpressionView.html Launch ExpressionView]<br />
* [http://maya:7575/ExpressionView/bin/ExpressionView.html?filename=../data/ALL.small.xml Launch ExpressionView with ALL data (8 modules)]<br />
* [http://maya:7575/ExpressionView/bin/ExpressionView.html?filename=../data/ALL.large.xml Launch ExpressionView with ALL data (108 modules)]<br />
<br />
= Screenshots = <br />
<gallery widths="200px" heights="109px" perrow="3"><br />
image:Expressionview.screenshot.1.png|Startup screen<br />
image:Expressionview.screenshot.2.png|Global view after loading dataset<br />
image:Expressionview.screenshot.3.png|Highlighting modules<br />
image:Expressionview.screenshot.4.png|Zoom functions<br />
image:Expressionview.screenshot.5.png|Highlighting genes (probes) and samples<br />
image:Expressionview.screenshot.6.png|GO and KEGG associations<br />
image:Expressionview.screenshot.7.png|Modules view emphasizing the underlying gene expression data<br />
image:Expressionview.screenshot.8.png|Global view without gene expression data<br />
image:Expressionview.screenshot.9.png|Experiment description<br />
</gallery><br />
<br />
= Download =<br />
<br />
<br />
= Tutorials =<br />
There are several tutorials describing how to use ExpressionView:<br />
<br />
== R package ==<br />
<br />
== Flash applet ==<br />
<br />
= Additional documentation =<br />
* [[pdf:Expressionview-ordering|Ordering algorithm]]<br />
* [http://maya:7575/ExpressionView/doc ActionScript source code documentation]<br />
* [[pdf:Expressionview-xml|XML file structure]]</div>Andreas