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

Pinned Loading

  1. cwl-commandlinetools cwl-commandlinetools Public

    Forked from mskcc/cwl-commandlinetools

    Central location for CWL CommandLineTools

    Common Workflow Language 5

  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 2

  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

Repositories

Showing 10 of 44 repositories
  • merge_fastq Public

    Package to merge multiple pair of pair-end fastq data

    msk-access/merge_fastq’s past year of commit activity
    Python 3 1 0 14 Updated Oct 28, 2024
  • chip-var Public

    Workflow for calling and annotating CHIP variants

    msk-access/chip-var’s past year of commit activity
    Common Workflow Language 0 AGPL-3.0 0 0 1 Updated Oct 21, 2024
  • postprocessing_variant_calls Public

    This repository helps with processing for variant calls made by a given caller

    msk-access/postprocessing_variant_calls’s past year of commit activity
    Python 0 MIT 2 6 1 Updated Oct 16, 2024
  • 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 2 AGPL-3.0 1 0 0 Updated Oct 15, 2024
  • 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 5 AGPL-3.0 3 6 1 Updated Oct 15, 2024
  • 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 4 Updated Oct 1, 2024
  • 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 0 1 2 4 Updated Oct 1, 2024
  • 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 Sep 7, 2024
  • 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 6 1 Updated Sep 5, 2024
  • 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 Aug 27, 2024

Top languages

Loading…

Most used topics

Loading…