broadinstitute

Official code repository for GATK versions 4 and up

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

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

Inferring CNV from Single-Cell RNA-Seq

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

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

GTEx & TOPMed data production and analysis pipelines

Pilon is an automated genome assembly improvement and variant detection tool

Spatial alignment of single cell transcriptomic data.

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

Keras package for deep residual networks

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

Warp Analysis Research Pipelines

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

web-based analysis tool for rare disease genomics

Ultrafast GPU-enabled QTL mapper

A structural variation pipeline for short-read sequencing

viral-ngs: command line tools and wrappers for processing raw viral genomic data

A software package for analyzing snapshots of developmental processes

Long read production pipelines

Cell Painting Gallery

Java tools for analyzing Drop-seq data

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

MuTect -- Accurate and sensitive cancer mutation detection

A package for designing compact and comprehensive capture probe sets.

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

Source code and related materials for the O'Reilly book

Hail helper functions for the gnomAD project and Translational Genomics Group

Documentation archive for GATK tools and workflows

Explore gnomAD datasets on the web

Spatial and multiomic visualization and analysis library

Pyro models of SARS-CoV-2 variants

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

viral-ngs: complete pipelines

Fast and exact gap-affine partial order alignment

GTEx Visualizations

Collection of analysis tools for quantitative trait loci

Fast, scalable, accurate and accessible Bayesian phylogenetics

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

Docker container for running the Terraform application

CLI for interacting with Cromwell servers

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

Scripts and utilities for analyzing tandem repeats (TRs).

Tutorials, workflows, and convenience scripts for Single Cell Portal

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