msk-access Goto Github PK

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access_artifacts

This repo tracts recurrent artifacts that we observe in MSK-ACCESS data

access_data_analysis

Scripts for downstream analysis plotting of pipeline output

access_qc_generation

Generation Quality Controls Files for MSK-ACCESS

access_utils

Miscelaneous Scripts for MSK-ACCESS workflows

athena

Provides HTML reports with detailed coverage analysis for clinical NGS data.

bam_collapsing

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

biometrics

Python package to calculate various sample contamination metrics.

chip-var

Workflow for calling and annotating CHIP variants

cookiecutter-pypackage

Cookiecutter template for a Python package.

copynumber_variation

cwl-commandlinetools

Central location for CWL CommandLineTools

cwl_pass_through

Blank CWL for Voyager Operators that don't use cwls.

cwl_subworkflows

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

deltamsi

DeltaMSI: AI-based screening for microsatellite instability in solid tumors

docker_multiple_tools

Containers for miscellaneous tools used by ACCESS workflows

docker_trim_galore

Dockerized Trim Galore

fgbio_postprocessing

Tools for fulcrum bam processing

genomenexus_annotation-pipeline

genotype_variants

Project to genotype SNV, INDEL and SV.

getbasecountsmultisample

igv_snapshot

merge_fastq

Package to merge multiple pair of pair-end fastq data

microsatellite_instability

msisensor-ct

Microsatellite instability (MSI) detection for cfDNA samples.

msisensor2

Microsatellite instability (MSI) detection for tumor only data.

msk-access.github.io

Documentation for MSK-ACCESS workflows

msk_lib

Misc. tools that may be useful for others at MSK.

mskaccess_operators

Operators for creating input JSON using provided metadata

multiqc

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