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@msk-access

CMO Cell-Free DNA (cfDNA) Informatics Team

This organization is created to host all the codebase related to cfDNA based assay in CMO at MSKCC
README.md

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  1. cwl-commandlinetools cwl-commandlinetools Public

    Forked from mskcc/cwl-commandlinetools

    Central location for CWL CommandLineTools

    Common Workflow Language 6

  2. access_data_analysis access_data_analysis Public

    Scripts for downstream analysis plotting of pipeline output

    R 7

  3. biometrics biometrics Public

    Python package to calculate various sample contamination metrics.

    Python 6 3

  4. nucleo nucleo Public

    Workflow that creates all the BAM files for the cfDNA assay based FASTQ file at MSK

    Common Workflow Language 3 1

  5. nucleo_qc nucleo_qc Public

    Quality Control Workflow for UMI based BAMs

    Common Workflow Language 1

  6. krewlyzer krewlyzer Public

    Feature extraction tools for circulating tumor DNA from GRCh37 aligned BAM files

    Python 1

Repositories

Showing 10 of 49 repositories
  • STRiDE Public

    MSK-ACCESS MSI calling tool

    msk-access/STRiDE’s past year of commit activity
    Python 0 MIT 0 0 0 Updated Feb 20, 2026
  • py-gbcms Public

    high-performance tool for extracting base counts and variant metrics from BAM files.

    msk-access/py-gbcms’s past year of commit activity
    Python 0 AGPL-3.0 0 0 0 Updated Feb 20, 2026
  • krewlyzer Public

    Feature extraction tools for circulating tumor DNA from GRCh37 aligned BAM files

    msk-access/krewlyzer’s past year of commit activity
    Python 1 AGPL-3.0 0 0 0 Updated Feb 14, 2026
  • sequence_qc Public

    Noise calculations from BAM file

    msk-access/sequence_qc’s past year of commit activity
    Python 0 1 6 2 Updated Feb 2, 2026
  • nucleo_qc Public

    Quality Control Workflow for UMI based BAMs

    msk-access/nucleo_qc’s past year of commit activity
    Common Workflow Language 1 Apache-2.0 0 0 0 Updated Jan 27, 2026
  • cwl_subworkflows Public

    A list of subworkflows used for MSK-ACCESS data processing.

    msk-access/cwl_subworkflows’s past year of commit activity
    Common Workflow Language 3 AGPL-3.0 1 0 1 Updated Jan 22, 2026
  • access_data_analysis Public

    Scripts for downstream analysis plotting of pipeline output

    msk-access/access_data_analysis’s past year of commit activity
    R 7 Apache-2.0 0 7 1 Updated Dec 16, 2025
  • biometrics Public

    Python package to calculate various sample contamination metrics.

    msk-access/biometrics’s past year of commit activity
    Python 6 3 6 2 Updated Nov 24, 2025
  • genotype_variants Public

    Project to genotype SNV, INDEL and SV.

    msk-access/genotype_variants’s past year of commit activity
    Python 1 4 0 0 Updated Sep 29, 2025
  • MultiQC_change_modules Public Forked from MultiQC/MultiQC

    Aggregate results from bioinformatics analyses across many samples into a single report.

    msk-access/MultiQC_change_modules’s past year of commit activity
    JavaScript 0 GPL-3.0 659 0 0 Updated Sep 22, 2025
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