Explore @mskcc Open Source projects

Memorial Sloan Kettering (@mskcc)

mskcc

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vcf2maf

Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms

facets

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 signatures

facets-suite

Utility functions for FACETS

ngs-filters

Filters for false-positive mutation calls in NGS

lohhla

Fork from https://bitbucket.org/mcgranahanlab/lohhla/src, modified for MSKCC needs

mimsi

Microsatellite Instability Classification using Multiple Instance Learning

roslin-variant

Roslin is a reproducible and reusable workflow for Cancer Genomic Sequencing Analysis

cbsp-hackathon

Computational Biology Summer Program Hackathon

Jupyter Notebook

tempo

CCS research pipeline to process WES and WGS TN pairs

Innovation-IMPACT-Pipeline

Framework to process and call somatic variation from NGS dataset generated using MSK-IMPACT assay

ACCESS-Pipeline

cfDNA Sequencing Pipeline with UMI

facets2n

Algorithm to implement Fraction and Allelic Copy number Estimate from Tumor/normal Sequencing using unmatched normal sample(s) for log ratio calculations

Marianas

Software for processing molecular barcoding (UMI)-based NGS data

cmo

Command-line tools for data analysts at the CMO

forte

Functional Observation of RNA Transcriptome Elements/Expression

tempoSig

Fitting mutational catalog to signatures with maximum likelihood

igo-demux

Demultiplex Illumina sequencer output via DRAGEN, create fastq files and launch pipelines

htstools

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 output

hermes

Data collection management and analysis of information

Medidata.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 CommandLineTools

Common Workflow Language

Halo_Melanoma_IL2

Code for Melanoma paper

igo-qc

LimsRest

the restful service used by the IGO LIMS

Medidata.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 IGO

igo-request-tracker

Tracks state of IGO projects

roslin-core

Core of the Roslin pipeline

beagle

Voyager Backend

smile-server

roslin-qc

redcap-linter

hera

First web app to be hosted on delphi.mskcc.org.

igo-genomics

pointer

Voyager Frontend

helix_filters_01

Workflows for post-pipeline data processing and file generation

dragen_util

Helper DRAGEN scripts

hera-sample-tracker

igo-sample-qc-backend

pluto-cwl

CWL workflows for helix filter scripts

concordance-workflow

artisan-fhir-server

roslin-helix

Documentation for Roslin/Helix Pipeline

variant_launch_validation

a legacy project to validate m/p/g files

ngs-stats

NGS Statistics Database with historical Picard Stats, IGO fastq.gz paths and Sequencer Start & Stop Times

sample-qc-node

vcf_accuracy

vcf accuracy evaluator using VT, BEDTOOLS, PyVCF, and TABIX

ridgeback

awsbatch_mock

AWSBatch Mock built for scaling tests

Chronos

Generate uuid's that will sort chronologically

common-domain

dotfiles

Unix dotfiles for users of MSK compute

smile-commons

Centralized configurations for checkstyle plugin and dependency management.

Waltz

Fast, efficient bam metrics, pileups and genotyping

GDD-Phase2

This is the Second Generation of Genome Derived Diagnosis AI Project

pipeline-kickoff

msisensor

process_fastq

This package will help process, merge and link fastq in user specified directory from manifest file

facets-preview-dev

neoantigen-pipeline

Pipeline for computing neoantigen qualities from DNA and RNA-Seq data

cHL-spatial-profiling

Code supporting results of cHL manuscript

DeepSig

Single-Base Substitution Mutational Signature Inference for WES and MSK-IMPACT

nf-fastq-plus

Generate IGO fastqs, bams, stats and fingerprinting