Ecosyste.ms: Awesome
An open API service indexing awesome lists of open source software.
Projects in Awesome Lists by mskcc
A curated list of projects in awesome lists by mskcc .
https://github.com/mskcc/maf_calc_tmb
give it a maf and target array size and target bed and it generates the tmb
Last synced: 12 Nov 2024
https://github.com/mskcc/losslessbam
temp. repo for losslessbam creation workflow
Last synced: 12 Nov 2024
https://github.com/mskcc/igo-static-pages
Static site content for IGO web applications.
Last synced: 12 Nov 2024
https://github.com/mskcc/external-samples-rest
Rest service to retrieve DMP samples for IGO
Last synced: 12 Nov 2024
https://github.com/mskcc/fireflask
flask site for our fireworks implementation
Last synced: 12 Nov 2024
https://github.com/mskcc/fero
Convert familiar MPGR files to beagle-friendly metadata json, importable into Voyager
Last synced: 12 Nov 2024
https://github.com/mskcc/ddp-spec-date-collector
Fetches clinical sample collection dates from ddp web service for given set of ids
Last synced: 12 Nov 2024
https://github.com/mskcc/dmp-bams
Draft of DMP-BAMs tool; may need to be merged into a different repo once done
Last synced: 12 Nov 2024
https://github.com/mskcc/process_fastq
This package will help process, merge and link fastq in user specified directory from manifest file
Last synced: 12 Nov 2024
https://github.com/mskcc/collect-qc
Collect QC (CQ) is pipeline agnostic tool to merge QC metrics
Last synced: 12 Nov 2024
https://github.com/mskcc/igo-delivery
Delivery email, symlinks and permissions for IGO projects
Last synced: 12 Nov 2024
https://github.com/mskcc/sif
Nextflow workflow for handling Structural Variants
Last synced: 12 Nov 2024
https://github.com/mskcc/igo-sample-submission-node
Sample Submission API written in node.js
Last synced: 12 Nov 2024
https://github.com/mskcc/vepcheck
Nextflow pipeline to check different vep version
Last synced: 12 Nov 2024
https://github.com/mskcc/penguin
ecDNA detection pipeline for MSK Sequencing Data
Last synced: 12 Nov 2024
https://github.com/mskcc/argos_report
Repository for ARGOS report (v1.0.1 Balto)
Last synced: 12 Nov 2024
https://github.com/mskcc/toil-elk
Template for running Toil on LSF HPC with ELK stack logging
Last synced: 12 Nov 2024
https://github.com/mskcc/odin
Module for variant calling and maf processing
Last synced: 12 Nov 2024
https://github.com/mskcc/rediscoverte
Pipeline for quantifying genome-wide TE expression in RNA sequencing data
Last synced: 12 Nov 2024
https://github.com/mskcc/fp-docker
Facets Preview Docker implementation for local use.
Last synced: 12 Nov 2024
https://github.com/mskcc/smile-label-generator
SMILE messaging service for handling CMO label generation
Last synced: 12 Nov 2024
https://github.com/mskcc/simba
Runs all thenextflow workflow scripts for IMPACT processing
Last synced: 12 Nov 2024
https://github.com/mskcc/smile-request-filter
CMO MetaDB Request Filter app
Last synced: 12 Nov 2024
https://github.com/mskcc/pluto
Utilities for pluto-cwl and helix_filters repos
Last synced: 12 Nov 2024
https://github.com/mskcc/redcap-data-dictionary-diff
A tool for analyzing and displaying the differences between two REDCap data dictionaries. Outputs into an Excel spreadsheet.
Last synced: 12 Nov 2024
https://github.com/mskcc/mjolnir-spec
Specification for the CI utility container
Last synced: 12 Nov 2024
https://github.com/mskcc/chl-pre-processing
Hodgkins specific HaloX code: pre-processing of Halo CSV data to project agnostic RDA files
Last synced: 12 Nov 2024
https://github.com/mskcc/triassic
Containers to faciliate the running of old (pre-disaster) JUNO scripts
Last synced: 12 Nov 2024
https://github.com/mskcc/cmo-scripts
A collection of decently modular bioinformatics scripts
Last synced: 12 Nov 2024
https://github.com/mskcc/odin-tmb
Code to compute the TMB score from an input MAF file and assay (gene-panel) value.
Last synced: 12 Nov 2024
https://github.com/mskcc/mobius
Until we find a better name: umbrella term for Argos Next Step
Last synced: 12 Nov 2024
https://github.com/mskcc/crispressotools
Tools to facilitate Crispresso Analysis
Last synced: 12 Nov 2024
https://github.com/mskcc/nats-messaging-go
Wrapper around Golang client for NATS.
Last synced: 12 Nov 2024
https://github.com/mskcc/agreto
Find wild-type sequences of neoantigens and run netMHCpan
Last synced: 12 Nov 2024
https://github.com/mskcc/natural-language-processing-with-deep-learning-in-healthcare
Last synced: 12 Nov 2024
https://github.com/mskcc/automation-data-pipeline-of-pathology-digital-slides
Last synced: 12 Nov 2024
https://github.com/mskcc/ppbc
Database based web application for biospecimen collection and storage. The application is to automate, standardize processes of biorepository at precision pathology biobanking center.
Last synced: 12 Nov 2024
https://github.com/mskcc/argos-cwl
A portable and reproducible pipeline for targeted analysis
Last synced: 12 Nov 2024