Difference between revisions of "ExpressionView"
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== Launch the ExpressionView Flash applet == | == Launch the ExpressionView Flash applet == | ||
| − | * [http:// | + | * [http://www2.unil.ch/cbg/software/expressionview/flash/ExpressionView.html Launch ExpressionView] |
| − | * [http:// | + | * [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)] |
| − | * [http:// | + | * [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)] |
| − | == Download the R package (includes the Flash applet)== | + | == Download the R package (includes the Flash applet) == |
| + | * [http://www2.unil.ch/cbg/software/expressionview/r/ExpressionView_0.2.1_windows.zip Windows binary package] | ||
| + | * [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] | ||
| + | * [http://www2.unil.ch/cbg/software/expressionview/r/ExpressionView_0.2.1_source.tar.gz Source package] | ||
== Download the stand-alone viewer (adobe AIR) == | == Download the stand-alone viewer (adobe AIR) == | ||
| − | If you prefer a stand-alone viewer, you can download and install the Adobe AIR build [http:// | + | 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> |
To run the program, you need the AIR runtime environment which you can get from [http://get.adobe.com/air Adobe].<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 to launch the viewer and load the data. | ExpressionView creates files associations to .evf files, allowing you to simply double-click on such files to launch the viewer and load the data. | ||
== Download sample data == | == Download sample data == | ||
| − | * [http:// | + | * [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). |
| − | * [http:// | + | * [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). |
= Screenshots = | = Screenshots = | ||
| Line 39: | Line 42: | ||
== R package == | == R package == | ||
| + | [[Media:Expressionview.tutorial.pdf|Getting started with ExpressionView]] | ||
== Flash applet == | == Flash applet == | ||
| + | |||
| + | == Installing the stand-alone version == | ||
= Additional documentation and downloads = | = Additional documentation and downloads = | ||
* [[Media:Expressionview.ordering.pdf|Ordering algorithm]] | * [[Media:Expressionview.ordering.pdf|Ordering algorithm]] | ||
| − | * [ | + | * [hhttp://www2.unil.ch/cbg/software/expressionview/doc ActionScript source code documentation] |
* [[Media:Expressionview.xmldescription.pdf|XML file structure]] | * [[Media:Expressionview.xmldescription.pdf|XML file structure]] | ||
* [[Media:Expressionview.largebitmapdata.tar.gz|ActionScript implementation of the LargeBitmapData class (allows to use bitmaps of arbitrary dimensions)]] | * [[Media:Expressionview.largebitmapdata.tar.gz|ActionScript implementation of the LargeBitmapData class (allows to use bitmaps of arbitrary dimensions)]] | ||
* [[Media:Expressionview.resizablepanel.tar.gz|ActionScript implementation of the ResizablePanel class (a panel with open, maximize, minimize, close and resize buttons)]] | * [[Media:Expressionview.resizablepanel.tar.gz|ActionScript implementation of the ResizablePanel class (a panel with open, maximize, minimize, close and resize buttons)]] | ||
Revision as of 07:19, 3 December 2009
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.
Launch and download
Launch the ExpressionView Flash applet
- Launch ExpressionView
- Launch ExpressionView with adult T-cell acute lymphocytic leukemia (ALL) data (8 modules)
- Launch ExpressionView with adult T-cell acute lymphocytic leukemia (ALL) data (108 modules)
Download the R package (includes the Flash applet)
- Windows binary package
- Mac OS X 32 bit binary package, Mac OS X 64 bit binary package
- Source package
Download the stand-alone viewer (adobe AIR)
If you prefer a stand-alone viewer, you can download and install the Adobe AIR build ExpressionView.air (right-click to download file).
To run the program, you need the AIR runtime environment which you can get from Adobe.
ExpressionView creates files associations to .evf files, allowing you to simply double-click on such files to launch the viewer and load the data.
Download sample data
- Gene expression profile of adult T-cell acute lymphocytic leukemia (ALL) with 8 modules (right-click to download file).
- Gene expression profile of adult T-cell acute lymphocytic leukemia (ALL) with 108 modules (right-click to download file).
Screenshots
Startup screen
Global view after loading dataset
Highlighting modules
Zoom functions
Highlighting genes (probes) and samples
GO and KEGG associations
Modules view emphasizing the underlying gene expression data
Global view without gene expression data
Experiment description
Tutorials
There are several tutorials describing how to use ExpressionView:
R package
Getting started with ExpressionView
Flash applet
Installing the stand-alone version
Additional documentation and downloads
- Ordering algorithm
- [hhttp://www2.unil.ch/cbg/software/expressionview/doc ActionScript source code documentation]
- XML file structure
- ActionScript implementation of the LargeBitmapData class (allows to use bitmaps of arbitrary dimensions)
- ActionScript implementation of the ResizablePanel class (a panel with open, maximize, minimize, close and resize buttons)
