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@mskcc Memorial Sloan Kettering

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    225 repositories

    • igo-demux

      Public
      Demultiplex Illumina sequencer output via DRAGEN, create fastq files and launch pipelines
      Python
      •
      Apache License 2.0
      •0•6•4•0•Updated Nov 18, 2024Nov 18, 2024

    • process_fastq

      Public
      This package will help process, merge and link fastq in user specified directory from manifest file
      Python
      •
      Other
      •0•0•0•16•Updated Nov 16, 2024Nov 16, 2024

    • smile-databricks-gateway

      Public
      Go
      •
      GNU Affero General Public License v3.0
      •0•0•0•0•Updated Nov 15, 2024Nov 15, 2024

    • forte

      Public
      Functional Observation of RNA Transcriptome Elements/Expression
      Nextflow
      •
      MIT License
      •0•7•21•3•Updated Nov 15, 2024Nov 15, 2024

    • smile-request-filter

      Public
      CMO MetaDB Request Filter app
      Java
      •
      GNU Affero General Public License v3.0
      •4•0•0•0•Updated Nov 15, 2024Nov 15, 2024

    • smile-label-generator

      Public
      SMILE messaging service for handling CMO label generation
      Java
      •
      GNU Affero General Public License v3.0
      •3•0•0•0•Updated Nov 15, 2024Nov 15, 2024

    • smile-server

      Public
      Java
      •4•2•78•1•Updated Nov 15, 2024Nov 15, 2024

    • smile-messaging-java

      Public
      CMO Messaging Library
      Java
      •
      GNU Affero General Public License v3.0
      •3•0•0•0•Updated Nov 15, 2024Nov 15, 2024

    • tempo

      Public
      CCS research pipeline to process WES and WGS TN pairs
      Groovy
      •5•12•49•8•Updated Nov 15, 2024Nov 15, 2024

    • smile-commons

      Public
      Centralized configurations for checkstyle plugin and dependency management.
      Java
      •
      GNU Affero General Public License v3.0
      •4•1•0•1•Updated Nov 15, 2024Nov 15, 2024

    • beagle

      Public
      Voyager Backend
      Python
      •5•2•97•20•Updated Nov 15, 2024Nov 15, 2024

    • smile-dashboard

      Public
      TypeScript
      •
      GNU Affero General Public License v3.0
      •8•0•0•0•Updated Nov 14, 2024Nov 14, 2024

    • LimsRest

      Public
      the restful service used by the IGO LIMS
      Java
      •2•2•5•4•Updated Nov 14, 2024Nov 14, 2024

    • neoantigen-pipeline

      Public
      Pipeline for computing neoantigen qualities from DNA and RNA-Seq data
      Python
      •
      MIT License
      •0•1•8•0•Updated Nov 14, 2024Nov 14, 2024

    • swabnseq

      Public
      Python
      •0•0•0•0•Updated Nov 14, 2024Nov 14, 2024

    • roslin-variant

      Public
      Roslin is a reproducible and reusable workflow for Cancer Genomic Sequencing Analysis
      pipelineprism
      Python
      •8•15•8•3•Updated Nov 13, 2024Nov 13, 2024

    • simba

      Public
      Runs all thenextflow workflow scripts for IMPACT processing
      Nextflow
      •
      MIT License
      •0•0•0•0•Updated Nov 13, 2024Nov 13, 2024

    • odin

      Public
      Module for variant calling and maf processing
      Python
      •
      MIT License
      •0•0•0•0•Updated Nov 13, 2024Nov 13, 2024

    • arrakis

      Public
      Abra realignment workflow
      Nextflow
      •
      MIT License
      •0•0•1•0•Updated Nov 13, 2024Nov 13, 2024

    • igo-delivery

      Public
      Delivery email, symlinks and permissions for IGO projects
      Python
      •
      Apache License 2.0
      •0•0•0•0•Updated Nov 12, 2024Nov 12, 2024

    • argos-cwl

      Public
      A portable and reproducible pipeline for targeted analysis
      Common Workflow Language
      •0•0•5•1•Updated Nov 11, 2024Nov 11, 2024

    • sif

      Public
      Nextflow workflow for handling Structural Variants
      Nextflow
      •
      MIT License
      •0•0•0•0•Updated Nov 11, 2024Nov 11, 2024

    • ridgeback

      Public
      Toil API
      Python
      •2•1•38•3•Updated Nov 11, 2024Nov 11, 2024

    • igo-sample-submission-node

      Public
      Sample Submission API written in node.js
      JavaScript
      •1•0•1•31•Updated Nov 7, 2024Nov 7, 2024

    • loki

      Public
      Workflow for handling CNV events
      Nextflow
      •
      MIT License
      •1•0•1•0•Updated Nov 7, 2024Nov 7, 2024

    • ngs-stats

      Public
      NGS Statistics Database with historical Picard Stats, IGO fastq.gz paths and Sequencer Start & Stop Times
      HTML
      •0•1•2•1•Updated Nov 6, 2024Nov 6, 2024

    • igo-lims-plugins

      Public
      Sapio LIMS customizations to workflows for IGO
      Java
      •0•2•1•7•Updated Nov 5, 2024Nov 5, 2024

    • igo-landing-page

      Public
      JavaScript
      •1•0•0•6•Updated Nov 5, 2024Nov 5, 2024

    • vepcheck

      Public
      Nextflow pipeline to check different vep version
      Nextflow
      •
      MIT License
      •0•0•0•0•Updated Nov 4, 2024Nov 4, 2024

    • Penguin

      Public
      ecDNA detection pipeline for MSK Sequencing Data
      Jupyter Notebook
      •0•0•0•0•Updated Oct 31, 2024Oct 31, 2024