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

Genomic Identification of Significant Targets in Cancer

This is basic GenePattern module written in Python 3. It can be taken as a Template for future modules. (click 'Use this template' to get started)

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

GenePattern Hierarchical Clustering module.

UMap or TSNE validation plots

Visualizes prediction results

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

Module for GSEA Julia Implementation

Imports data from the Gene Expression Omnibus (GEO)

Actual creation of the Elastic Principa Graph in the STREAM scRNASeq Trajectory analysis, packaged as a GenePattern module

Detect differentially expressed genes between pairs of trajectory branches

A configurable heat map viewer that provides users with several options for manipulating and visualizing array-based data

GenePattern module wrapping igv.js

scVelo wrapper module for GenePattern

Views results of hierarchical clustering.

Repo for the HISAT2 .ndexer module which creates indices for the HISAT2.aligner module

Salmon quantification wrapper module for GenePattern.

HTSeq (0.11.2) wrapper module: Counting reads in features with 'htseq-count'