Discover broadinstitute/gnomad_qc Open Source project

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

1,691

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.

990

picard

Inferring CNV from Single-Cell RNA-Seq

965

infercnv

558

keras-rcnn

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

GTEx & TOPMed data production and analysis pipelines

554

gtex-pipeline

Pilon is an automated genome assembly improvement and variant detection tool

334

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.

293

Tangram

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

249

ssGSEA2.0

237

ABC-Enhancer-Gene-Prediction

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

WDL Analysis Research Pipelines

201

warp

Viral genomics analysis pipelines

200

viral-ngs

web-based analysis tool for rare disease genomics

180

seqr

A structural variation pipeline for short-read sequencing

176

gatk-sv

Ultrafast GPU-enabled QTL mapper

170

tensorqtl

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

159

ichorCNA

159

long-read-pipelines

Long read production pipelines

A software package for analyzing snapshots of developmental processes

140

wot

ml4h

depmap_omics

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

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

110

xtermcolor

Java tools for analyzing Drop-seq data

104

Drop-seq

MuTect -- Accurate and sensitive cancer mutation detection

100

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

A package for designing compact and comprehensive capture probe sets.

catch

Documentation archive for GATK tools and workflows

gatk-docs

oncotator

Explore gnomAD datasets on the web

gnomad-browser

TypeScript

gtex-viz

GTEx Visualizations

JavaScript

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

2020_scWorkshop

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

Shell

cromshell

CLI for interacting with Cromwell servers

viral-ngs: complete pipelines

cellpainting-gallery

Cell Painting Gallery

viral-pipelines

Tutorials, workflows, and convenience scripts for Single Cell Portal

single_cell_portal

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

gistic2

MATLAB

sam

workbench identity and access management

dsde-deep-learning

DSDE Deep Learning Club

A C++14 library for NGS data formats

gamgee

C++

wdl-ide

Rich IDE support for Workflow Description Language

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

gtex-v8

Collection of analysis tools for quantitative trait loci

pyqtl

GPU implementation of ARD NMF

SignatureAnalyzer-GPU

Fast and exact gap-affine partial order alignment

poasta

Rust

Celligner_ms

cell-health

Predicting Cell Health with Morphological Profiles

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

PANOPLY

gatk-protected

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

strain-level analysis tools

StrainGE

firecloud-orchestration

Python and UNIX CLI utilities to simplify interaction with the NIH/NCI Genomics Data Commons

gdctools

Python interface to the Sectigo Certificate Manager REST API

python-cert_manager

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

str-analysis

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

adapt

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

2019_scWorkshop

TeX

chronos

Modeling of time series data for CRISPR KO experiments

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

fiss

Python bindings for Bifrost with a NetworkX compatible API

pyfrost

Documents used for workshops on single cell analysis

single_cell_analysis

Image classification for imaging flow cytometry.

deepometry

Processed Cell Painting Data for the LINCS Drug Repurposing Project

lincs-cell-painting

rawls

Rawls service for DSDE

Fast, scalable, accurate and accessible Bayesian phylogenetics

delphy

C++

firepony

Efficient base quality score recalibrator for NGS data

Cuda

protigy

Proteomics Toolset for Integrative Data Analysis

GATK-for-Microbes

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

seqr-loading-pipelines

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

BipolarCell2016

cromwell-tools

COVID-19 Diagnostic Processing Dashboard

covid19-testing

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

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

gtex-single-nucleus-reference

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

flipbook

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

AwesomeGenomics

firecloud-ui

FireCloud user interface for web browsers.

Clojure

BARD

BioAssay Research Database

Groovy

wdltool

Vim syntax highlighting for WDL

vim-wdl

Vim Script

SpliceAI-lookup

Website for checking SpliceAI and Pangolin scores:

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

palantir-workflows

Epigenomics Program pipeline to analyze SHARE-seq data.

epi-SHARE-seq-pipeline

Crowd Authentication Plugin for Wordpress

wordpress-crowd-plugin

PHP

mix_seq_ms

Code associated with MIX-seq manuscript

imaging-platform-pipelines

Cell Painting and other pipelines from the Imaging Platform

wdl-runner

Easily run WDL workflows on GCP

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

widdler

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

cms

Code to calculate regional missense constraint

regional_missense_constraint

scRNA-Seq

Public collaboration of Scalable Single Cell Analytics

scalable_analytics

Multimodal data loader compatible with pytorch and tensorflow

ml4ht_data_source

Discoverability for gene search 🧬 🔍

100

gene-hints