Difference between revisions of "ExpressionView"
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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. | 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. | ||
| − | = | + | = Demos = |
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* [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://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://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)] | * [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)] | ||
| + | * [http://www2.unil.ch/cbg/software/expressionview/flash/ExpressionView.html Launch ExpressionView] | ||
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| + | = Requirements and installation = | ||
== Download the R package (includes the Flash applet) == | == Download the R package (includes the Flash applet) == | ||
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* [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://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://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). | * [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). | ||
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| + | = License = | ||
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| + | The ExpressionView package is licensed under the GNU General Public License, version 2 or later. For details, see http://www.gnu.org/licenses/old-licenses/gpl-2.0.html. | ||
= Screenshots = | = Screenshots = | ||
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</gallery> | </gallery> | ||
| − | = Tutorials = | + | = Documentation = |
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| + | == Tutorials == | ||
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. | 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. | ||
| − | == R package == | + | === R package === |
* [[Media:Expressionview.tutorial.pdf|Getting started with ExpressionView]] | * [[Media:Expressionview.tutorial.pdf|Getting started with ExpressionView]] | ||
* [[Media:Expressionview.ordering.pdf|Ordering algorithm]] | * [[Media:Expressionview.ordering.pdf|Ordering algorithm]] | ||
| − | == Flash applet == | + | === Flash applet === |
* [[Media:Expressionview.quickhelp.pdf|Quick help (pdf)]] | * [[Media:Expressionview.quickhelp.pdf|Quick help (pdf)]] | ||
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* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.getting.started.mov Getting started (video tutorial, 6 minutes)] | * [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.getting.started.mov Getting started (video tutorial, 6 minutes)] | ||
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* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.view.mov Fullscreen feature (video tutorial, 1 minute)] | * [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.view.mov Fullscreen feature (video tutorial, 1 minute)] | ||
| − | == Installing the stand-alone version == | + | === Installing the stand-alone version === |
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.standalone.mov Stand-alone installation (video tutorial, 2 minutes)] | * [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.standalone.mov Stand-alone installation (video tutorial, 2 minutes)] | ||
Revision as of 16:35, 26 May 2010
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.
Contents
Demos
- 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)
- Launch ExpressionView
Requirements and installation
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
Note that ExpressionView requires the eisa R 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).
License
The ExpressionView package is licensed under the GNU General Public License, version 2 or later. For details, see http://www.gnu.org/licenses/old-licenses/gpl-2.0.html.
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
Documentation
Tutorials
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.
R package
Flash applet
- Getting started (video tutorial, 6 minutes)
- Using the tables (video tutorial, 6 minutes)
- Modular view (video tutorial, 4 minutes)
- Fullscreen feature (video tutorial, 1 minute)
Installing the stand-alone version
Additional documentation and downloads
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 Flex website.
- ExpressionView source code (for the Flash applet)
- ActionScript source code documentation
- Documentation of the XML file structure
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 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.
