GenePattern 3.9.6 Release Notes

Released January 22, 2016

GenePattern 3.9.6 requires Java 7+.

System requirements and known issues are detailed on the following pages. 

Bug Fixes and Enhancements

  • Password fields are now rendered properly on the job submit form.
  • Drag and drop of directories from the Files tab is now working for parameters that accept multiple files.

Admin Support

  • Added automatic R Package installer

Modules Released Since September 25, 2015

  • CLSFileCreator - A tool to create a class label (CLS) file.    
  • CsvToFcs - Converts a Comma separated values (CSV) file to a Flow Cytometry Standard (FCS) file.
  • GSEA - Gene Set Enrichment Analysis.
  • GSEALeadingEdgeViewer - Leading Edge Viewer for GSEA results.
  • GSEAPreranked - Runs the gene set enrichment analysis against a user-supplied ranked list of genes.
  • MergeHTSeqCounts - Merges HTSeq read count data files into one file
  • PreprocessReadCounts - Preprocess RNA-Seq count data in a GCT file so that it is suitable for use in GenePattern analyses.
  • ReannotateGCT - Reannotate a GCT file's "Description" column with data from a CHIP file
  • SOMClusterViewer - Visualize clusters created with the SOM algorithm