Discover mskcc/dotfiles Open Source project

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

roslin-variant

Computational Biology Summer Program Hackathon

cbsp-hackathon

Jupyter Notebook

tempo

CCS research pipeline to process WES and WGS TN pairs

Groovy

Innovation-IMPACT-Pipeline

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

Perl

ACCESS-Pipeline

cfDNA Sequencing Pipeline with UMI

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

facets2n

Marianas

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

Command-line tools for data analysts at the CMO

cmo

Functional Observation of RNA Transcriptome Elements/Expression

forte

Nextflow

tempoSig

Fitting mutational catalog to signatures with maximum likelihood

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

igo-demux

A Laravel implementation of the REDCap DDP (Dynamic Data Pull) middleware.

htstools

C++

redcap-ddp-laravel

PHP

vcf2tsv

a tool that takes the output files of different callers and creates maf-like, row-based output

Data collection management and analysis of information

hermes

JavaScript

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

the restful service used by the IGO LIMS

LimsRest

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.

Medidata.RWS.NET.Standard

facetsAPI

Sapio LIMS customizations to workflows for IGO

igo-lims-plugins

Tracks state of IGO projects

igo-request-tracker

JavaScript

roslin-core

Core of the Roslin pipeline

beagle

smile-server

roslin-qc

redcap-linter

hera

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

igo-genomics

pointer

helix_filters_01

Workflows for post-pipeline data processing and file generation

dragen_util

Helper DRAGEN scripts

Shell

hera-sample-tracker

igo-sample-qc-backend

CWL workflows for helix filter scripts

pluto-cwl

concordance-workflow

Documentation for Roslin/Helix Pipeline

artisan-fhir-server

PHP

roslin-helix

variant_launch_validation

a legacy project to validate m/p/g files

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

ngs-stats

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

sample-qc-node

JavaScript

vcf_accuracy

ridgeback

Toil API

AWSBatch Mock built for scaling tests

awsbatch_mock

Chronos

Generate uuid's that will sort chronologically

common-domain

Domain objects

Centralized configurations for checkstyle plugin and dependency management.

smile-commons

Fast, efficient bam metrics, pileups and genotyping

Waltz

This is the Second Generation of Genome Derived Diagnosis AI Project

GDD-Phase2

pipeline-kickoff

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

msisensor

C++

process_fastq

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

facets-preview-dev

neoantigen-pipeline

Code supporting results of cHL manuscript

cHL-spatial-profiling

DeepSig

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