Pinned Repositories
CellBender
CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.
cromwell
Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments
gatk
Official code repository for GATK versions 4 and up
gtex-pipeline
GTEx & TOPMed data production and analysis pipelines
infercnv
Inferring CNV from Single-Cell RNA-Seq
keras-rcnn
Keras package for region-based convolutional neural networks (RCNNs)
keras-resnet
Keras package for deep residual networks
picard
A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
pilon
Pilon is an automated genome assembly improvement and variant detection tool
ssGSEA2.0
Single sample Gene Set Enrichment analysis (ssGSEA) and PTM Enrichment Analysis (PTM-SEA)
Broad Institute's Repositories
broadinstitute/gatk
Official code repository for GATK versions 4 and up
broadinstitute/cromwell
Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments
broadinstitute/seqr
web-based analysis tool for rare disease genomics
broadinstitute/gatk-sv
A structural variation pipeline for short-read sequencing
broadinstitute/long-read-pipelines
Long read production pipelines
broadinstitute/depmap_omics
What you need to process the Quarterly DepMap-Omics releases from Terra
broadinstitute/gnomad-browser
Explore gnomAD datasets on the web
broadinstitute/gnomad_qc
broadinstitute/viral-pipelines
viral-ngs: complete pipelines
broadinstitute/sam
workbench identity and access management
broadinstitute/rawls
Rawls service for DSDE
broadinstitute/seqr-loading-pipelines
hail-based pipelines for annotating variant callsets and exporting them to elasticsearch
broadinstitute/palantir-workflows
Utility workflows for the DSP hydro.gen team (formerly palantir)
broadinstitute/epi-SHARE-seq-pipeline
Epigenomics Program pipeline to analyze SHARE-seq data.
broadinstitute/ddp-study-server
Pepper Study Server
broadinstitute/datarepo-helm
A helm repo for Broad Data Science Platforms helm charts
broadinstitute/juniper
broadinstitute/datarepo-helm-definitions
Helm deployment specific values and definitions for Dev, Integration and Prod
broadinstitute/scp-ingest-pipeline
File Ingest Pipeline for Single Cell Portal
broadinstitute/cpg
Cell painting gallery
broadinstitute/dig-dug-portal
broadinstitute/MDL-workflows
Workflow, utilities and other artefacts developed by or for the Methods Development Lab at the Broad Institute
broadinstitute/openidc-terra-proxy
OpenIDC proxy to be used for all Terra services
broadinstitute/dig-aggregator-methods
Monorepo of methods implemented for the Aggregator
broadinstitute/2021_09_01_VarChAMP
broadinstitute/broad-epi-workflows-collection
This repo contains WDL workflows written by the Epigenomics program.
broadinstitute/CellCap
Interpret perturbation responses from scRNA-seq perturbation experiments
broadinstitute/igv.js
Embeddable genomic visualization component based on the Integrative Genomics Viewer
broadinstitute/jati
DSL support library based on nom.
broadinstitute/TerraWorkflows