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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 604

  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 373

  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 361

Repositories

Showing 10 of 1375 repositories
  • rawls Public

    Rawls service for DSDE

    broadinstitute/rawls’s past year of commit activity
    Scala 25 BSD-3-Clause 4 0 4 Updated Apr 18, 2025
  • celldega Public

    Spatial omics analysis and visualization library

    broadinstitute/celldega’s past year of commit activity
    Jupyter Notebook 5 0 1 14 Updated Apr 18, 2025
  • palantir-workflows Public

    Utility workflows for the DSP hydro.gen team (formerly palantir)

    broadinstitute/palantir-workflows’s past year of commit activity
    WDL 23 BSD-3-Clause 8 4 3 Updated Apr 18, 2025
  • depmap_omics Public

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

    broadinstitute/depmap_omics’s past year of commit activity
    HTML 115 22 3 2 Updated Apr 18, 2025
  • depmap-portal Public

    Code for the DepMap portal at depmap.org

    broadinstitute/depmap-portal’s past year of commit activity
    Python 8 BSD-2-Clause 1 0 10 Updated Apr 18, 2025
  • pyops-service-toolkit Public

    Shared Python utilities that help with interacting with Terra, TDR, BigQuery, and GCP to name a few.

    broadinstitute/pyops-service-toolkit’s past year of commit activity
    Python 2 0 0 0 Updated Apr 18, 2025
  • jump_hub Public

    The one-stop-shop for Morphological Profiling and JUMP Cell-Painting

    broadinstitute/jump_hub’s past year of commit activity
    Python 4 CC0-1.0 2 9 0 Updated Apr 18, 2025
  • ml4h Public
    broadinstitute/ml4h’s past year of commit activity
    Python 132 25 30 (1 issue needs help) 22 Updated Apr 18, 2025
  • gatk Public

    Official code repository for GATK versions 4 and up

    broadinstitute/gatk’s past year of commit activity
    Java 1,794 604 1,246 (8 issues need help) 138 Updated Apr 18, 2025
  • BEClust3D Public
    broadinstitute/BEClust3D’s past year of commit activity
    Jupyter Notebook 0 0 0 8 Updated Apr 18, 2025
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