Memorial Sloan Kettering

New York, NY, USA

Pinned Repositories

facets
Algorithm to implement Fraction and Copy number Estimate from Tumor/normal Sequencing.
Language:R139 75 18665
facets-suite
Utility functions for FACETS
Language:R34 73 3825
iCallSV
A Framework to call Structural Variants from NGS based datasets
Language:Python3 6 01
lohhla
Fork from https://bitbucket.org/mcgranahanlab/lohhla/src, modified for MSKCC needs
Language:R28 37 1310
mimsi
Microsatellite Instability Classification using Multiple Instance Learning
Language:Python19 6 35
mutation-signatures
Create mutation signatures from MAF's, and decompose them into Stratton signatures
Language:R60 78 330
ngs-filters
Filters for false-positive mutation calls in NGS
Language:R30 45 1121
RNAseqDB
Language:Perl139 61 1441
roslin-variant
Roslin is a reproducible and reusable workflow for Cancer Genomic Sequencing Analysis
Language:Python15 31 828
vcf2maf
Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms
Language:Perl372 79 318216

Memorial Sloan Kettering's Repositories

mskcc/forte
Functional Observation of RNA Transcriptome Elements/Expression
Language:Nextflow70
mskcc/igo-demux
Demultiplex Illumina sequencer output via DRAGEN, create fastq files and launch pipelines
Language:Python6 5 230
mskcc/beagle
Voyager Backend
Language:Python2 10 3385
mskcc/facets-preview
Load, review and adjust facets fits
Language:R2 1 1
mskcc/igo-lims-plugins
Sapio LIMS customizations to workflows for IGO
Language:Java2 13 50
mskcc/LimsRest
the restful service used by the IGO LIMS
Language:Java2 7 472
mskcc/smile-server
Language:Java2 4 9974
mskcc/DeepSig
Single-Base Substitution Mutational Signature Inference for WES and MSK-IMPACT
Language:HTML1
mskcc/fp-docker
Facets Preview Docker implementation for local use.
Language:R1 6 11
mskcc/igo-genomics
Language:Vue1 8 240
mskcc/neoantigen-pipeline
Pipeline for computing neoantigen qualities from DNA and RNA-Seq data
Language:Python1 6 360
mskcc/process_fastq
This package will help process, merge and link fastq in user specified directory from manifest file
Language:Python1 3 0
mskcc/ridgeback
Toil API
Language:Python1 13 792
mskcc/smile-commons
Centralized configurations for checkstyle plugin and dependency management.
Language:Java1 3 04
mskcc/argos_report
Repository for ARGOS report (v1.0.1 Balto)
Language:CSS0 12 00
mskcc/igo-sample-submission-node
Sample Submission API written in node.js
Language:JavaScript0 9 111
mskcc/smile-dashboard
Language:TypeScript0 4 08
mskcc/AGFusion
Python package to annotate and visualize gene fusions.
Language:Python2 0
mskcc/beagle_cli
Beagle API Command Line Utility
Language:Python12 111
mskcc/igo-delivery
Delivery email, symlinks and permissions for IGO projects
Language:Python5 0
mskcc/igo-marketplace-login
Login application
Language:JavaScript7 01
mskcc/MetaFusion
Metafusion_forte
Language:Python2 4
mskcc/MetaFusion-Clinical
mskcc/odin
Module for variant calling and maf processing
Language:Python10 1
mskcc/Penguin
ecDNA detection pipeline for MSK Sequencing Data
Language:Jupyter Notebook
mskcc/phoenix
Phoenix is Module 1 from ARGOS
Language:Nextflow12 1
mskcc/smile-databricks-gateway
Language:Go
mskcc/smile-label-generator
SMILE messaging service for handling CMO label generation
Language:Java3 03
mskcc/smile-messaging-java
CMO Messaging Library
Language:Java3 03
mskcc/smile-request-filter
CMO MetaDB Request Filter app
Language:Java2 04