Skip to content
@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

Pinned Loading

  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 3 1

Repositories

Showing 10 of 50 repositories
  • STRiDE Public

    Microsatellite Instability prediction for MSK-ACCESS cfDNA sequencing.MSK-ACCESS MSI calling tool

    msk-access/STRiDE's past year of commit activity
    Python 0 MIT 0 0 1 Updated Oct 8, 2026
  • gbcms Public

    A high-performance orientation-aware genotype counting system for genomic variants

    msk-access/gbcms's past year of commit activity
    Python 2 AGPL-3.0 0 34 0 Updated Oct 8, 2026
  • kreview Public

    Advanced cfDNA Fragmentomics Core Evaluation Engine

    msk-access/kreview's past year of commit activity
    Python 3 0 3 0 Updated Sep 17, 2026
  • 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 11, 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 3 AGPL-3.0 1 0 0 Updated Aug 26, 2026
  • uncollapsed_bam_generation Public

    Workflow for making MSK-ACCESS standard binary alignment mapping file.

    msk-access/uncollapsed_bam_generation's past year of commit activity
    Common Workflow Language 0 2 1 1 Updated Jul 24, 2026
  • nucleo Public

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

    msk-access/nucleo's past year of commit activity
    Common Workflow Language 3 1 0 0 Updated Jul 8, 2026
  • bam_collapsing Public

    Workflow for collapsing of standard binary alignment mapping file generated by MSK-ACCESS

    msk-access/bam_collapsing's past year of commit activity
    Common Workflow Language 1 1 2 4 Updated Jul 8, 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 Jul 8, 2026
  • cwl-commandlinetools Public Forked from mskcc/cwl-commandlinetools

    Central location for CWL CommandLineTools

    msk-access/cwl-commandlinetools's past year of commit activity
    Common Workflow Language 6 AGPL-3.0 3 6 2 Updated Jul 8, 2026
View all repositories

Top languages

Loading…

Most used topics

Loading…