Memorial Sloan Kettering

vcf2maf

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

mimsi

Microsatellite Instability Classification using Multiple Instance Learning

tempo

CCS research pipeline to process WES and WGS TN pairs

igo-demux

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

toil

A scalable, efficient, cross-platform and easy-to-use workflow engine in pure Python

beagle

Voyager Backend

igo-lims-plugins

Sapio LIMS customizations to workflows for IGO

LimsRest

the restful service used by the IGO LIMS

smile-server

cHL-spatial-profiling

Code supporting results of cHL manuscript

igo-genomics

NeoAntigen-Pipeline

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

ngs-stats

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

process_fastq

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

ridgeback

Toil API

argos_report

Repository for ARGOS report (v1.0.1 Balto)

igo-sample-submission-node

Sample Submission API written in node.js

smile-dashboard

arrakis

Abra realignment workflow

beagle_cli

Beagle API Command Line Utility

fp-docker

Facets Preview Docker implementation for local use.

igo-10X-DB

this is code to parse and store 10X Cellranger data into ngs_stats and LIMS

igo-delivery

Delivery email, symlinks and permissions for IGO projects

igo-run-qc-node

igo-sample-qc-node

Sample QC with nodejs backend

jira-backup

Script to backup your boards on jira

loki

Workflow for handling CNV events

sif

Nextflow workflow for handling Structural Variants

simba

Runs all thenextflow workflow scripts for IMPACT processing

smile-label-generator

SMILE messaging service for handling CMO label generation