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
New York, NY
Pinned Repositories
access_data_analysis
Scripts for downstream analysis plotting of pipeline output
access_qc_generation
Generation Quality Controls Files for MSK-ACCESS
biometrics
Python package to calculate various sample contamination metrics.
cwl-commandlinetools
Central location for CWL CommandLineTools
cwl_subworkflows
A list of subworkflows used for MSK-ACCESS data processing.
GetBaseCountsMultiSample
merge_fastq
Package to merge multiple pair of pair-end fastq data
MultiQC
Aggregate results from bioinformatics analyses across many samples into a single report.
nucleo
Workflow that creates all the BAM files for the cfDNA assay based FASTQ file at MSK
nucleo_qc
Quality Control Workflow for UMI based BAMs
CMO Cell-Free DNA (cfDNA) Informatics Team's Repositories
msk-access/access_data_analysis
Scripts for downstream analysis plotting of pipeline output
msk-access/biometrics
Python package to calculate various sample contamination metrics.
msk-access/cwl-commandlinetools
Central location for CWL CommandLineTools
msk-access/merge_fastq
Package to merge multiple pair of pair-end fastq data
msk-access/nucleo
Workflow that creates all the BAM files for the cfDNA assay based FASTQ file at MSK
msk-access/cwl_subworkflows
A list of subworkflows used for MSK-ACCESS data processing.
msk-access/access_qc_generation
Generation Quality Controls Files for MSK-ACCESS
msk-access/chip-var
Workflow for calling and annotating CHIP variants
msk-access/genotype_variants
Project to genotype SNV, INDEL and SV.
msk-access/nucleo_qc
Quality Control Workflow for UMI based BAMs
msk-access/postprocessing_variant_calls
This repository helps with processing for variant calls made by a given caller
msk-access/sequence_qc
Noise calculations from BAM file
msk-access/.github
msk-access/access_artifacts
This repo tracts recurrent artifacts that we observe in MSK-ACCESS data
msk-access/athena
Provides HTML reports with detailed coverage analysis for clinical NGS data.
msk-access/bam_collapsing
Workflow for collapsing of standard binary alignment mapping file generated by MSK-ACCESS
msk-access/bedtools_samtools
msk-access/copynumber_variation
msk-access/cwl_pass_through
Blank CWL for Voyager Operators that don't use cwls.
msk-access/DeltaMSI
DeltaMSI: AI-based screening for microsatellite instability in solid tumors
msk-access/genomenexus_annotation-pipeline
msk-access/igv_snapshot
msk-access/microsatellite_instability
msk-access/msisensor-ct
Microsatellite instability (MSI) detection for cfDNA samples.
msk-access/msk-access.github.io
Documentation for MSK-ACCESS workflows
msk-access/mskaccess_operators
Operators for creating input JSON using provided metadata
msk-access/mutect1
msk-access/resources
Resource files for running MSK-ACCESS workflows
msk-access/structural_variation
msk-access/uncollapsed_bam_generation
Workflow for making MSK-ACCESS standard binary alignment mapping file.