Broad Institute

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

This is a set of data models for the A2F KP and other resources by the Flannick lab.

BE3D public repository

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kustomizations for current gnomad project kubernetes deployments

Permutect, an incredibly efficient deep learning architecture for somatic and germline variant calling

Code for the DepMap portal at depmap.org

GTEx & TOPMed data production and analysis pipelines

Warp Analysis Research Pipelines

Cell Painting Gallery

Website displaying aggregated info about gene-disease relationships @ genelookup.broadinstitute.org

An online portal for exploring tandem repeats (TRs) genome-wide.

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

Project to create metadata that is harmonized across the Cell Painting Gallery

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Dataproc lifecycle management for Hail jobs — Docker image + WDL workflow

Explore gnomAD datasets on the web

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This repo will contain the code for training DINO models and extracting features

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

Official code repository for GATK versions 4 and up

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Workflow, utilities and other artefacts developed by or for the Methods Development Lab at the Broad Institute

Collection of analysis tools for quantitative trait loci

Scripts used to process data for the first McCarroll lab BICAN manuscript

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

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