GenePattern Modules


Click the Html or Pdf icons to view a module's documentation.

Modules in the repository can be installed on a local GenePattern server. Most of these modules are also installed on the public GenePattern server.

View by Category:

NameTypeAvailability
COPA
Perform Cancer Outlier Profile Analysis (COPA)
Pdf  Version: 1
Gene List Selection * Public Server Only
ClassNeighbors
Select genes that most closely resemble a profile
Pdf  Version: 1
Gene List Selection Module Repository
ComparativeMarkerSelection
Identify differentially expressed genes that can discriminate between distinct classes of samples.
Html  Version: 10
Gene List Selection Module Repository
COPA
Performs Cancer Outlier Profile Analysis (COPA)
Pdf  Version: 1
Gene List Selection Module Repository
DESeq2
A Differential Expression workflow for RNA-Seq data based on the DESeq2 package from Bioconductor
Html  Version: 0.4
Gene List Selection Module Repository
ExtractComparativeMarkerResults
Creates a derived dataset and feature list file from the results of ComparativeMarkerSelection
Pdf  Version: 4
Gene List Selection Module Repository
GeneNeighbors
Select genes that most closely resemble a continuous profile (e.g., another gene)
Pdf  Version: 4
Gene List Selection Module Repository
GSEA
Gene Set Enrichment Analysis
Html  Version: 19.0.25
Gene List Selection Module Repository
GSEAPreranked
Runs the gene set enrichment analysis against a user-supplied ranked list of genes.
Html  Version: 6.0.5
Gene List Selection Module Repository
SelectFeaturesColumns
Takes a 'column slice' from a .res, .gct, .snp, .cn, .loh, .odf, or .cls file.
Pdf  Version: 4
Gene List Selection Module Repository
SelectFeaturesRows
Generate a .res, .gct, .snp, .cn, .loh, or .odf file containing only specified features (i.e. rows).
Pdf  Version: 4
Gene List Selection Module Repository