CMO Cell-Free DNA (cfDNA) Informatics Team's repositories
resources
Resource files for running MSK-ACCESS workflows
athena
Provides HTML reports with detailed coverage analysis for clinical NGS data.
puma_biliary_tract_summit_trial
Data for Targeting HER2 mutant advanced biliary tract cancers with neratinib: results from the SUMMIT ‘basket’ trial
PyVCF
A Variant Call Format reader for Python.
docker_multiple_tools
Containers for miscellaneous tools used by ACCESS workflows
access_utils
Miscelaneous Scripts for MSK-ACCESS workflows
spectrum
Package for downstream analysis of results generated by ACCESS workflows
msk_lib
Misc. tools that may be useful for others at MSK.
fgbio_postprocessing
Tools for fulcrum bam processing
cookiecutter-pypackage
Cookiecutter template for a Python package.
msisensor2
Microsatellite instability (MSI) detection for tumor only data.
templates
WIP - starting point for writing Dockerfiles and CWL code from scratch
docker_trim_galore
Dockerized Trim Galore
python_bed_lookup
Rapid lookups by coordinate from a bed file