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assoctool

Association tool

bcbio-nextgen

Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis

bcftools

This is the official development repository for BCFtools. To compile, the develop branch of htslib is needed: git clone --branch=develop git://github.com/samtools/htslib.git htslib

bdcatalyst-demo

blockly

The web-based visual programming editor.

bowtie2

A fast and sensitive gapped read aligner

bwa

Burrow-Wheeler Aligner for pairwise alignment between DNA sequences

cgl-docker-lib

cgprna

cgrdna

Project to document the NGS DNA variation calling pipelines in use at DCEG

cgrfunctional

chimerascan

Automatically exported from code.google.com/p/chimerascan

clonevol

Inferring and visualizing clonal evolution in multi-sample cancer sequencing

code_docker_lib

Dockerized tools for the Center for Omics Discovery and Epidemiology

cutadapt

cutadapt removes adapter sequences from sequencing reads

cwl_apps

Collection of CWL apps descriptions. Some are in progress.

dbgap2x

deconstructsigs

deconstructSigs

deepblues

Artificially generated 12-bar blues melodies using Recurrent Neural Networks

demo-gwas

CWL repository

dockerfiles

ensembl-tools

Ensembl tools including the VEP

epigenomics_cwl

SCREW: A Reproducible Workflow for Single-Cell Epigenomics

excerpt

Software for preprocessing, filtering, alignment, and reporting of smallRNA-seq datasets

facets

Algorithm to implement Fraction and Copy number Estimate from Tumor/normal Sequencing.

fusioncatcher

Somatic fusion genes finder for RNA-seq data

gatk

GATK4 development

gatk-protected

GATK Official Release Repository: contains the core MIT-licensed GATK framework, plus "protected" tools restricted to non-commercial use only

gatk-protected-1

GATK4 development of the license-protected part of the toolkit

gene-expression-and-heart-failure

Differential expression & pathway analysis of heart failure