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.
Please note that GenePattern releases are now hosted on GitHub along with our source code.
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
HCA Notebook Workspace & GenePattern Notebook Workspace:
New Feature and Update Highlights:
Full release notes can be found on the GenePattern Notebook website.