CMO Cell-Free DNA (cfDNA) Informatics Team

All

44 repositories

nucleo
Public
Workflow that creates all the BAM files for the cfDNA assay based FASTQ file at MSK
umi bam msk-access
Common Workflow Language
•
Other
•1•3•0•0•Updated Nov 7, 2024Nov 7, 2024
uncollapsed_bam_generation
Public
Workflow for making MSK-ACCESS standard binary alignment mapping file.
umi cwl ctdna cfdna cwl-workflow workflow
Common Workflow Language
•
Other
•2•0•1•4•Updated Nov 7, 2024Nov 7, 2024
cwl_subworkflows
Public
A list of subworkflows used for MSK-ACCESS data processing.
common-workflow-language cwl-workflow workflow
Common Workflow Language
•
GNU Affero General Public License v3.0
•1•2•0•0•Updated Nov 7, 2024Nov 7, 2024
merge_fastq
Public
Package to merge multiple pair of pair-end fastq data
fastq-files
Python
•
Other
•1•3•0•14•Updated Nov 1, 2024Nov 1, 2024
bam_collapsing
Public
Workflow for collapsing of standard binary alignment mapping file generated by MSK-ACCESS
ctdna cwl-workflow fgbio workflow duplex bam-collapsing msk-access
Common Workflow Language
•
Other
•1•0•2•4•Updated Nov 1, 2024Nov 1, 2024
chip-var
Public
Workflow for calling and annotating CHIP variants
Common Workflow Language
•
GNU Affero General Public License v3.0
•0•0•0•1•Updated Oct 21, 2024Oct 21, 2024
postprocessing_variant_calls
Public
This repository helps with processing for variant calls made by a given caller
Python
•
MIT License
•2•0•6•1•Updated Oct 16, 2024Oct 16, 2024
cwl-commandlinetools
Public
Central location for CWL CommandLineTools
command common-workflow-language cwl cwltool
Common Workflow Language
•
GNU Affero General Public License v3.0
•3•5•6•1•Updated Oct 15, 2024Oct 15, 2024
access_data_analysis
Public
Scripts for downstream analysis plotting of pipeline output
r msk-access python analysis data-analysis
R
•
Apache License 2.0
•0•7•6•1•Updated Sep 5, 2024Sep 5, 2024
nucleo_qc
Public
Quality Control Workflow for UMI based BAMs
chip cfdna
Common Workflow Language
•
Apache License 2.0
•0•1•0•0•Updated Aug 27, 2024Aug 27, 2024
igv_snapshot
Public
Python
•0•0•0•0•Updated Aug 13, 2024Aug 13, 2024
bedtools_samtools
Public
0•0•0•0•Updated Aug 13, 2024Aug 13, 2024
biometrics
Public
Python package to calculate various sample contamination metrics.
contamination-detection python
Python
•
Other
•2•6•6•1•Updated Jul 27, 2024Jul 27, 2024
genotype_variants
Public
Project to genotype SNV, INDEL and SV.
genotyping msk-access
Python
•
Other
•4•1•0•2•Updated Jul 26, 2024Jul 26, 2024
genomenexus_annotation-pipeline
Public
Dockerfile
•0•0•0•0•Updated Mar 19, 2024Mar 19, 2024
mutect1
Public
Shell
•0•0•0•0•Updated Jan 17, 2024Jan 17, 2024
DeltaMSI
Public
DeltaMSI: AI-based screening for microsatellite instability in solid tumors
Python
•
GNU General Public License v3.0
•1•0•0•0•Updated Dec 28, 2023Dec 28, 2023
msisensor-ct
Public
Microsatellite instability (MSI) detection for cfDNA samples.
Makefile
•
GNU General Public License v3.0
•3•0•0•0•Updated Oct 9, 2023Oct 9, 2023
sequence_qc
Public
Noise calculations from BAM file
noise-detection
Python
•
Other
•0•0•6•1•Updated Jul 6, 2023Jul 6, 2023
cwl_pass_through
Public
Blank CWL for Voyager Operators that don't use cwls.
Common Workflow Language
•0•0•0•0•Updated Jun 14, 2023Jun 14, 2023
access_qc_generation
Public
Generation Quality Controls Files for MSK-ACCESS
multiqc cwl-workflow
Common Workflow Language
•
Apache License 2.0
•1•1•5•2•Updated Dec 26, 2022Dec 26, 2022
microsatellite_instability
Public
Makefile
•
Other
•0•0•1•2•Updated Dec 26, 2022Dec 26, 2022
copynumber_variation
Public
Makefile
•
Other
•0•0•1•3•Updated Dec 26, 2022Dec 26, 2022
structural_variation
Public
Makefile
•
Other
•0•0•1•2•Updated Dec 26, 2022Dec 26, 2022
mskaccess_operators
Public
Operators for creating input JSON using provided metadata
Python
•
Other
•0•0•0•2•Updated Dec 26, 2022Dec 26, 2022
msk-access.github.io
Public
Documentation for MSK-ACCESS workflows
msk-access
JavaScript
•
Apache License 2.0
•1•0•0•7•Updated Nov 9, 2022Nov 9, 2022
access_artifacts
Public
This repo tracts recurrent artifacts that we observe in MSK-ACCESS data
Apache License 2.0
•0•0•0•0•Updated Nov 3, 2022Nov 3, 2022
resources
Public
Resource files for running MSK-ACCESS workflows
Apache License 2.0
•1•0•0•0•Updated Aug 1, 2022Aug 1, 2022
.github
Public
0•0•0•0•Updated Jul 29, 2022Jul 29, 2022
athena
Public
Provides HTML reports with detailed coverage analysis for clinical NGS data.
Python
•
MIT License
•2•0•0•0•Updated Jun 7, 2022Jun 7, 2022