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vcf2maf
Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoformsfacets
Algorithm to implement Fraction and Copy number Estimate from Tumor/normal Sequencing.RNAseqDB
mutation-signatures
Create mutation signatures from MAF's, and decompose them into Stratton signaturesfacets-suite
Utility functions for FACETSngs-filters
Filters for false-positive mutation calls in NGSlohhla
Fork from https://bitbucket.org/mcgranahanlab/lohhla/src, modified for MSKCC needsmimsi
Microsatellite Instability Classification using Multiple Instance Learningroslin-variant
Roslin is a reproducible and reusable workflow for Cancer Genomic Sequencing Analysiscbsp-hackathon
Computational Biology Summer Program Hackathontempo
CCS research pipeline to process WES and WGS TN pairsInnovation-IMPACT-Pipeline
Framework to process and call somatic variation from NGS dataset generated using MSK-IMPACT assayACCESS-Pipeline
cfDNA Sequencing Pipeline with UMIfacets2n
Algorithm to implement Fraction and Allelic Copy number Estimate from Tumor/normal Sequencing using unmatched normal sample(s) for log ratio calculationsMarianas
Software for processing molecular barcoding (UMI)-based NGS datacmo
Command-line tools for data analysts at the CMOforte
Functional Observation of RNA Transcriptome Elements/ExpressiontempoSig
Fitting mutational catalog to signatures with maximum likelihoodigo-demux
Demultiplex Illumina sequencer output via DRAGEN, create fastq files and launch pipelineshtstools
redcap-ddp-laravel
A Laravel implementation of the REDCap DDP (Dynamic Data Pull) middleware.vcf2tsv
a tool that takes the output files of different callers and creates maf-like, row-based outputhermes
Data collection management and analysis of informationMedidata.RWS.NET
Medidata.RWS.NET is a comprehensive, fluent .NET API library for Medidata RAVE Web Services (RWS). It handles a large portion of the boilerplate C# code you'd normally have to write in order to communicate with RWS, allowing you to get up and running faster.cwl-commandlinetools
Central location for CWL CommandLineToolsHalo_Melanoma_IL2
Code for Melanoma paperigo-qc
LimsRest
the restful service used by the IGO LIMSMedidata.RWS.NET.Standard
Medidata.RWS.NET.Standard is a comprehensive, fluent .NET Standard 2.0 API library for Medidata RAVE Web Services (RWS). It handles a large portion of the boilerplate C# code you'd normally have to write in order to communicate with RWS, allowing you to get up and running faster.facetsAPI
igo-lims-plugins
Sapio LIMS customizations to workflows for IGOigo-request-tracker
Tracks state of IGO projectsroslin-core
Core of the Roslin pipelinebeagle
Voyager Backendsmile-server
roslin-qc
redcap-linter
hera
First web app to be hosted on delphi.mskcc.org.igo-genomics
pointer
Voyager Frontendhelix_filters_01
Workflows for post-pipeline data processing and file generationdragen_util
Helper DRAGEN scriptshera-sample-tracker
igo-sample-qc-backend
pluto-cwl
CWL workflows for helix filter scriptsconcordance-workflow
artisan-fhir-server
roslin-helix
Documentation for Roslin/Helix Pipelinevariant_launch_validation
a legacy project to validate m/p/g filesngs-stats
NGS Statistics Database with historical Picard Stats, IGO fastq.gz paths and Sequencer Start & Stop Timessample-qc-node
vcf_accuracy
vcf accuracy evaluator using VT, BEDTOOLS, PyVCF, and TABIXridgeback
Toil APIawsbatch_mock
AWSBatch Mock built for scaling testsChronos
Generate uuid's that will sort chronologicallycommon-domain
Domain objectsdotfiles
Unix dotfiles for users of MSK computesmile-commons
Centralized configurations for checkstyle plugin and dependency management.Waltz
Fast, efficient bam metrics, pileups and genotypingGDD-Phase2
This is the Second Generation of Genome Derived Diagnosis AI Projectpipeline-kickoff
msisensor
process_fastq
This package will help process, merge and link fastq in user specified directory from manifest fileneoantigen-pipeline
Pipeline for computing neoantigen qualities from DNA and RNA-Seq datacHL-spatial-profiling
Code supporting results of cHL manuscriptDeepSig
Single-Base Substitution Mutational Signature Inference for WES and MSK-IMPACTnf-fastq-plus
Generate IGO fastqs, bams, stats and fingerprintingLove Open Source and this site? Check out how you can help us