The public GenePattern server hosted by the GenePattern team was officially migrated to the Amazon cloud: https://cloud.genepattern.org on January 1, 2019. To support this migration, GenePattern now requires that all modules be run in a Docker container.
More information about our use of Docker and the administration of GenePattern in the cloud can be found in our wiki on GitHub.
MutPanning - New - MutPanning identifies driver genes based on their abundance of nonsynonymous mutations and their increased number of mutations in unusual nucleotide contexts that deviate from the background mutational process.
Kallisto - New- Running Kallisto with basic parameters to perfomr pseudoalignment using a human transcriptome index (GRCh 38 from the Ensembl Archive Release 95)
CellFie - New - Metabolic task modeling with CellFie
MethylationCNVAnalysis - New - Methylation array preprocessing with the minfi R package and copy-number variation analysis with the conumee R package. Compatible with both 450k or EPIC array data.
GSEAPreranked - Updated to use the GSEA v4.0.2 code base. Updated to give access to MSigDB v7.0. OpenJDK 11 port. Java code moved into the GSEA Desktop code base.
GSEA - Updated to use the GSEA v4.0.2 code base. Updated to give access to MSigDB v7.0. OpenJDK 11 port. Java code moved into the GSEA Desktop code base.
ssGSEAProjection - Updated to give access to MSigDB v7.0. Unified the Gene Set DB selector parameters and better downloading of MSigDB files. Removed Java dependency. Added a no-normalize option as the default.
ConstellationMap - Updated for MSigDB v7.0
DESeq2 - Updated to output a counts table file
New Feature and Update Highlights: