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absolute

Contains gp-unit tests for ABSOLUTE modules

absolute.review

Archive of the now deprecated ABSOLUTE.review genepattern module

absolute.summarize

Archived of deprecated ABSOLUTE.summarize module

affystexpressionfilecreator

Creates a GCT file from a set of CEL files from Affymetrix ST arrays.

ampliconsuite

Wraps the AmpliconSuite-pipeline workflow to identify one or more connected genomic regions which have copy number amplifications.

ampliconsuiteaggregator

Aggregates the results from AmpliconSuite

bulkatacseq.preprocess

bwa_module

This is the repository for the GenePattern BWA module

cbswrapperpipeline

A one step pipeline that runs CBS

ccal-noir

Clone of CCAL with calls to R removed

cellfie

clsfilecreator

This a GenePattern Javascript visualizer that creates a CLS file from a GCT file.

combat

Performs batch correction on a dataset containing multiple batches

combat_seq

Batch effect adjustment based on negative binomial regression for RNA sequencing count data. Credits: https://github.com/zhangyuqing/ComBat-seq

common_module_code

This repository contains the shared code used by the GenePattern modules.

community-amaretto

Docker build and module artifacts for community-amaretto module

comparativemarkerselection

Identify differentially expressed genes that can discriminate between distinct classes of samples.

computational-translational-genomics

Software tools used in the preparation of the computational translational genomics (tentative name)

conos.cluster

Clustering using Conos (part 2/3)

conos.preprocess

Read, preprocess, and project data using Conos (step 1/3)

conos.visualizegeneexpression

Visualize expression of genes of interest after Conos.Cluster has been ran.

constellationmap

A downstream visualization and analysis tool for gene set enrichment results with interactive web visualizer

containerized-server

Scripts and build files to create containerized (Docker, Singularity) GP server stacks (compose, kubernetes)

conumee_cnv_analysis_module

convert.alevin

Convert alevin wrapper module for GenePattern.

coxregression

Cox regression using clinical data and .cls file

cuffcompare

cuffdiff

GenePattern Cuffdiff module.

cufflinks

Cufflinks - Assembles transcripts, estimates abundances, and tests for differential expression and regulation in RNA-seq samples

cufflinkscuffmergepipeline