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Programming Environment

Programming Language EnvironmentGenePattern provides a simple application interface that gives users access to computational analysis methods and tools, regardless of their computational experience. GenePattern also provides a programmatic interface that makes those analysis modules available to computational biologists and developers from Java, MATLAB, and R.

The GenePattern server provides links to a GenePattern library for each programming environment. You can use the library functions to run analysis modules on the server, check the job status, and retrieve analysis result files. The analysis results files are then available for processing in the programming environment of your choice.

The GenePattern server also provides documentation of each analysis module and its parameters. Alternatively, you can use the GenePattern application interface to generate the code (Java, MATLAB, or R) required to run the desired analysis.

The GenePattern libraries provide access to GenePattern from the Java, MATLAB, and R programming environments. If you are writing analysis modules to be added to GenePattern, you can use Java, MATLAB, R, or any other programming language.