Discover broadinstitute/gdctools Open Source project

Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments

1,604

cromwell

A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.

953

picard

Keras package for region-based convolutional neural networks (RCNNs)

923

keras-rcnn

Inferring CNV from Single-Cell RNA-Seq

548

infercnv

509

gtex-pipeline

GTEx & TOPMed data production and analysis pipelines

Pilon is an automated genome assembly improvement and variant detection tool

323

pilon

Keras package for deep residual networks

306

keras-resnet

CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.

294

CellBender

Spatial alignment of single cell transcriptomic data.

243

Tangram

Single sample Gene Set Enrichment analysis (ssGSEA) and PTM Enrichment Analysis (PTM-SEA)

219

ssGSEA2.0

218

ABC-Enhancer-Gene-Prediction

Cell type specific enhancer-gene predictions using ABC model (Fulco, Nasser et al, Nature Genetics 2019)

WDL Analysis Research Pipelines

183

warp

Viral genomics analysis pipelines

183

viral-ngs

web-based analysis tool for rare disease genomics

180

seqr

A structural variation pipeline for short-read sequencing

164

gatk-sv

Estimating tumor fraction in cell-free DNA from ultra-low-pass whole genome sequencing.

157

ichorCNA

156

tensorqtl

Ultrafast GPU-enabled QTL mapper

A software package for analyzing snapshots of developmental processes

142

wot

Long read production pipelines

130

long-read-pipelines

ml4h

xtermcolor

Python library for terminal color support (including 256-color support)

Java tools for analyzing Drop-seq data

104

Drop-seq

What you need to process the Quarterly DepMap-Omics releases from Terra

100

depmap_omics

MuTect -- Accurate and sensitive cancer mutation detection

mutect

Source code and related materials for the O'Reilly book

genomics-in-the-cloud

Hail helper functions for the gnomAD project and Translational Genomics Group

gnomad_methods

Pyro models of SARS-CoV-2 variants

pyro-cov

Documentation archive for GATK tools and workflows

gatk-docs

A package for designing compact and comprehensive capture probe sets.

catch

Explore gnomAD datasets on the web

gnomad-browser

oncotator

gtex-viz

single_cell_portal_core

Rails/Docker application for the Broad Institute's single cell RNA-seq data portal

Ruby

PhylogicNDT

Docker container for running the Terraform application

docker-terraform

Shell

cromshell

CLI for interacting with Cromwell servers

Code and data repository for the 2020 physalia course on single cell RNA sequencing.

2020_scWorkshop

Shell

viral-pipelines

viral-ngs: complete pipelines

gnomad_qc

Tutorials, workflows, and convenience scripts for Single Cell Portal

single_cell_portal

workbench identity and access management

sam

Genomic Identification of Significant Targets in Cancer (GISTIC), version 2

gistic2

MATLAB

gamgee

A C++14 library for NGS data formats

C++

dsde-deep-learning

DSDE Deep Learning Club

Notebooks and scripts for reproducing analyses and figures from the V8 GTEx Consortium paper

gtex-v8

GPU implementation of ARD NMF

SignatureAnalyzer-GPU

Rich IDE support for Workflow Description Language

wdl-ide

Predicting Cell Health with Morphological Profiles

Celligner_ms

cellpainting-gallery

Cell Painting Gallery

cell-health

Obsolete/Legacy GATK repository -- go to https://github.com/broadinstitute/gatk instead

gatk-protected

Collection of analysis tools for quantitative trait loci

pyqtl

Repository for the Broad Institute Proteogenomic Data Analysis Center (PGDAC) established by the NIH Clinical Proteomics Tumor Analysis Consortium (CPTAC)

PANOPLY

python-cert_manager

Python interface to the Sectigo Certificate Manager REST API

strain-level analysis tools

StrainGE

firecloud-orchestration

Repo for Physalia course Analysis of Single Cell RNA-Seq data

2019_scWorkshop

TeX

fiss

FireCloud Service Selector (FISS) -- Python bindings and CLI for FireCloud execution engine

Documents used for workshops on single cell analysis

single_cell_analysis

Image classification for imaging flow cytometry.

deepometry

Efficient base quality score recalibrator for NGS data

firepony

Cuda

adapt

A package for designing activity-informed nucleic acid diagnostics for viruses.

Python bindings for Bifrost with a NetworkX compatible API

pyfrost

Scripts and utilities related to analyzing short tandem repeats (STRs).

str-analysis

rawls

Rawls service for DSDE

Proteomics Toolset for Integrative Data Analysis

protigy

seqr-loading-pipelines

hail-based pipelines for annotating variant callsets and exporting them to elasticsearch

Processed Cell Painting Data for the LINCS Drug Repurposing Project

lincs-cell-painting

A collection of Python clients and accessory scripts for interacting with the Cromwell

BipolarCell2016

cromwell-tools

Methods to use SNPs or gene expression to classify single cell RNAseq to reference profiles

single_cell_classification

VariantBam

Filtering and profiling of next-generational sequencing data using region-specific rules

Makefile

longbow

Annotation and segmentation of MAS-seq data

Modeling of time series data for CRISPR KO experiments

chronos

Code repository for the snRNA-seq cross-tissue atlas project

gtex-single-nucleus-reference

COVID-19 Diagnostic Processing Dashboard

covid19-testing

Cancer Data Science's go to place for excellent genomics tools and packages

AwesomeGenomics

GATK-for-Microbes

FireCloud user interface for web browsers.

firecloud-ui

Clojure

BARD

BioAssay Research Database

Groovy

flipbook

A tool that lets you quickly flip through images in a local directory and record notes or answer questions about each one.

Utility workflows for the DSP hydro.gen team (formerly palantir)

palantir-workflows

wdltool

Vim syntax highlighting for WDL

vim-wdl

Vim Script

wordpress-crowd-plugin

Crowd Authentication Plugin for Wordpress

PHP

epi-SHARE-seq-pipeline

Epigenomics Program pipeline to analyze SHARE-seq data.

Code associated with MIX-seq manuscript

mix_seq_ms

widdler

A command-line tool for executing, managing, and querying WDL workflows on Cromwell servers.

Website for checking SpliceAI and Pangolin scores:

SpliceAI-lookup

Cell Painting and other pipelines from the Imaging Platform

imaging-platform-pipelines

wdl-runner

Easily run WDL workflows on GCP

Composite of Multiple Signals: tests for selection in meiotically recombinant populations

cms

scRNA-Seq

Public collaboration of Scalable Single Cell Analytics

scalable_analytics

Easy batch submission of adhoc jobs onto GCP

sparklespray

Code to calculate regional missense constraint

regional_missense_constraint

Shiny app for visualization, exploration of mouse brain single cell gene expression

dropviz

gnomad_lof

100

hdf5-java-bindings

java bindings for hdf5