Repositories list

• vepcheck

  Public
  Nextflow pipeline to check different vep version

  Nextflow

  •

  MIT License

  •0•0•0•0•Updated Nov 4, 2024Nov 4, 2024

• LimsRest

  Public
  the restful service used by the IGO LIMS

  Java

  •2•2•5•5•Updated Nov 4, 2024Nov 4, 2024

• beagle

  Public
  Voyager Backend

  Python

  •5•2•97•20•Updated Nov 4, 2024Nov 4, 2024

• argos-cwl

  Public
  A portable and reproducible pipeline for targeted analysis

  Common Workflow Language

  •0•0•5•1•Updated Nov 4, 2024Nov 4, 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 4, 2024Nov 4, 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 1, 2024Nov 1, 2024

• loki

  Public
  Workflow for handling CNV events

  Nextflow

  •

  MIT License

  •1•0•1•0•Updated Nov 1, 2024Nov 1, 2024

• igo-sample-submission-node

  Public
  Sample Submission API written in node.js

  JavaScript

  •1•0•1•31•Updated Nov 1, 2024Nov 1, 2024

• tempo

  Public
  CCS research pipeline to process WES and WGS TN pairs

  Groovy

  •5•12•49•7•Updated Oct 31, 2024Oct 31, 2024

• Penguin

  Public
  ecDNA detection pipeline for MSK Sequencing Data

  Jupyter Notebook

  •0•0•0•0•Updated Oct 31, 2024Oct 31, 2024

• neoantigen-pipeline

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

  Python

  •

  MIT License

  •0•1•8•2•Updated Oct 30, 2024Oct 30, 2024

• facets-preview

  Public
  Load, review and adjust facets fits

  R

  •3•2•3•0•Updated Oct 30, 2024Oct 30, 2024

• forte

  Public
  Functional Observation of RNA Transcriptome Elements/Expression

  Nextflow

  •

  MIT License

  •0•7•21•3•Updated Oct 30, 2024Oct 30, 2024

• ridgeback

  Public
  Toil API

  Python

  •2•1•38•5•Updated Oct 30, 2024Oct 30, 2024

• beagle_cli

  Public
  Beagle API Command Line Utility

  Python

  •1•0•8•3•Updated Oct 29, 2024Oct 29, 2024

• smile-databricks-gateway

  Public
  Go

  •

  GNU Affero General Public License v3.0

  •0•0•0•0•Updated Oct 29, 2024Oct 29, 2024

• igo-genomics

  Public
  Vue

  •0•1•3•0•Updated Oct 28, 2024Oct 28, 2024

• smile-dashboard

  Public
  TypeScript

  •

  GNU Affero General Public License v3.0

  •8•0•0•3•Updated Oct 24, 2024Oct 24, 2024

• 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 Oct 24, 2024Oct 24, 2024

• argos_report

  Public
  Repository for ARGOS report (v1.0.1 Balto)

  CSS

  •0•0•0•0•Updated Oct 22, 2024Oct 22, 2024

• odin

  Public
  Module for variant calling and maf processing

  Python

  •

  MIT License

  •0•0•0•0•Updated Oct 10, 2024Oct 10, 2024

• DeepSig

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

  HTML

  •

  MIT License

  •0•1•0•0•Updated Oct 9, 2024Oct 9, 2024

• igo-delivery

  Public
  Delivery email, symlinks and permissions for IGO projects

  Python

  •

  Apache License 2.0

  •0•0•0•0•Updated Oct 9, 2024Oct 9, 2024

• igo-lims-plugins

  Public
  Sapio LIMS customizations to workflows for IGO

  Java

  •0•2•1•7•Updated Oct 2, 2024Oct 2, 2024

• phoenix

  Public
  Phoenix is Module 1 from ARGOS

  Nextflow

  •0•0•1•0•Updated Oct 2, 2024Oct 2, 2024

• fp-docker

  Public
  Facets Preview Docker implementation for local use.

  R

  •0•1•1•0•Updated Oct 2, 2024Oct 2, 2024

• smile-server

  Public
  Java

  •4•2•77•3•Updated Oct 2, 2024Oct 2, 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 Oct 2, 2024Oct 2, 2024

• smile-request-filter

  Public
  CMO MetaDB Request Filter app

  Java

  •

  GNU Affero General Public License v3.0

  •4•0•0•1•Updated Oct 2, 2024Oct 2, 2024

• AGFusion

  Public
  Python package to annotate and visualize gene fusions.

  Python

  •

  MIT License

  •25•0•0•0•Updated Oct 1, 2024Oct 1, 2024