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cuffmerge

cuffnorm_cuffquant

Archive of old Cufflinks modules

cummerbund

cuzcatlan

Edwin Juarez's support library for GenePattern

dapple

Disease Association Protein-Protein Link Evaluator (Broad hosted algorithm)

deseq2

A Differential Expression workflow for RNA-Seq data based on the DESeq2 package from Bioconductor

deseq2.demo

Demo wrapper module for the DESeq2 R package

deseq2toodf

This module will turn a TXT file into ComparativeMarkerSelectionViewer-compatible ODF file

diffdatasets

differential-expression-modalities

These are some modalities for differential expression analysis.

differentialexpressionviewer

Visualizes the results of ComparativeMarkerSelection

diffex

GenePattern module to perform differential expression using Pearson correlation or information coefficient.

diffmodule

GP module for comparing test results with known good files.

discover

GenePattern Module which implements the DiSCoVER algorithm

docker-amaretto

Docker container and module wrapper for Amaretto from the Gavaert Lab at Stanford (http://med.stanford.edu/gevaertlab/software.html)

docker-aws-common-scripts

common scripts for docker/aws batch containers used for GenePattern modules

docker-cogaps

docker-download-from-gdc

GenePattern docker container for the download from gdc module

docker-gistic

Docker container for GISTIC 2.0.23

docker-hisat2

Docker container for hisat2 module

docker-java17

docker-java17openjdk

docker-java18

Docker container for java 18 (orackle jdk)

docker-java18openjdk

docker-mutsigcv

GenePattern container for MutSigCV module on docker and/or AWS Batch

docker-openjdk_11

Docker container for OpenJDK 11 on GenePattern, extending from the AdoptOpenJDK base Dockerfile.

docker-perl52

Perl 5.20 container for GenePattern modules on Docker and/or AWS Batch

docker-python36

Python 3.6.2 docker container for GenePattern modules running on AWSBatch

docker-python37

Python 3.7 docker container for GenePattern modules running on AWSBatch

docker-r-2-10

genepattern docker/aws batch container for R2.10 modules