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@broadinstitute

Broad Institute

Broad Institute of MIT and Harvard

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  1. gatk gatk Public

    Official code repository for GATK versions 4 and up

    Java 1.8k 602

  2. picard picard Public

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

    Java 1k 372

  3. cromwell cromwell Public

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

    Scala 1k 360

Repositories

Showing 10 of 1354 repositories
  • dig-dug-portal Public
    broadinstitute/dig-dug-portal’s past year of commit activity
    Vue 2 BSD-3-Clause 1 1 0 Updated Mar 22, 2025
  • pbs-analysis Public

    Scripts for analyzing ChIP-seq and related datatypes with binning and PBS

    broadinstitute/pbs-analysis’s past year of commit activity
    R 1 1 1 1 Updated Mar 22, 2025
  • dig-aggregator-methods Public

    Monorepo of methods implemented for the Aggregator

    broadinstitute/dig-aggregator-methods’s past year of commit activity
    Python 1 BSD-3-Clause 2 0 7 Updated Mar 22, 2025
  • depmap-portal Public

    Code for the DepMap portal at depmap.org

    broadinstitute/depmap-portal’s past year of commit activity
    Python 7 BSD-2-Clause 1 0 6 Updated Mar 22, 2025
  • single_cell_portal_core Public

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

    broadinstitute/single_cell_portal_core’s past year of commit activity
    Ruby 67 BSD-3-Clause 26 0 3 Updated Mar 21, 2025
  • xipher Public

    Tools for calling X-inactivation in scRNA-seq data

    broadinstitute/xipher’s past year of commit activity
    R 0 MIT 0 0 1 Updated Mar 21, 2025
  • workbench-libs Public

    Workbench utility libraries

    broadinstitute/workbench-libs’s past year of commit activity
    Scala 9 4 0 3 Updated Mar 21, 2025
  • sherlock Public

    DSP DevOps's deployment source-of-truth service

    broadinstitute/sherlock’s past year of commit activity
    Go 1 BSD-3-Clause 0 0 14 Updated Mar 21, 2025
  • EmmaEmb Public
    broadinstitute/EmmaEmb’s past year of commit activity
    Python 10 MIT 0 0 0 Updated Mar 21, 2025
  • seqr Public

    web-based analysis tool for rare disease genomics

    broadinstitute/seqr’s past year of commit activity
    Python 185 AGPL-3.0 89 48 3 Updated Mar 21, 2025
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