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ampliconclassifier

Classify output of AmpliconArchitect to detect types of focal amplifications present

bwa

Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

chm13

The complete sequence of a human genome

consensustme

ConsensusTME Gene Sets and R Script

cufflinks

gatk

Official code repository for GATK versions 4 and up

gatk4-somatic-cnvs

This repo is archived, these workflows will be housed in the GATK repository under the scripts directory. These workflows are also organized in Dockstore in the GATK Best Practices Workflows collection.

gatk4-somatic-snvs-indels

This repo has been archived, these workflows are still available in the GATK repository under the scripts directory. The workflows are also organized in Dockstore in the GATK Best Practices Workflows collection.

glass

GLASS consortium

juncbase

Junction Based Analysis of Splicing Events for RNA-Seq

learn-wdl

Educational materials for learning WDL

miso

MISO: Mixture of Isoforms model for RNA-Seq isoform quantitation

prada2

pyclone

Probabilistic model for inferring clonal population structure from deep NGS sequencing.

rsem

RSEM: accurate quantification of gene and isoform expression from RNA-Seq data

sccnautils

Functions to analyze copy number aberrations in single-cell data

tcellextrect

trinityrnaseq

Trinity RNA-Seq de novo transcriptome assembly

xcell

Cell types enrichment analysis