48 open source projects by broadinstitute

Pilon is an automated genome assembly improvement and variant detection tool

Inferring CNV from Single-Cell RNA-Seq

GTEx & TOPMed data production and analysis pipelines

Viral genomics analysis pipelines

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

MuTect -- Accurate and sensitive cancer mutation detection

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

Docker container for running the Terraform application

Official code repository for GATK versions 4 and up

Source code and related materials for the O'Reilly book

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

Prediction pipeline to generate prognosis predictors for Ebola Virus Disease

BioAssay Research Database

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.

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

Keras package for deep residual networks

DSDE Deep Learning Club

workbench identity and access management

Documents used for workshops on single cell analysis

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

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

A structural variation pipeline for short-read sequencing

No description, website, or topics provided.

A package for designing compact and comprehensive capture probe sets.

Ultrafast GPU-based QTL mapper

Workflow Description Language - Specification and Implementations

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

web-based analysis tool for rare disease genomics

Pyro models of SARS-CoV-2 variants

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

Tutorials, workflows, and convenience scripts for Single Cell Portal

GTEx Visualizations

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

GPU implementation of ARD NMF

No description, website, or topics provided.

Python bindings for Bifrost with a NetworkX compatible API

Efficient base quality score recalibrator for NGS data

FireCloud user interface for web browsers.

Explore gnomAD datasets on the web

CLI for interacting with Cromwell servers

Image classification for imaging flow cytometry.

A C++14 library for NGS data formats

No description, website, or topics provided.

Spatial alignment of single cell transcriptomic data.

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

Java tools for analyzing Drop-seq data

Rich IDE support for Workflow Description Language