Repositories list

• argos-cwl

  Public
  A portable and reproducible pipeline for targeted analysis

  Common Workflow Language

  •0•0•5•2•Updated Jan 10, 2025Jan 10, 2025

• Penguin

  Public
  ecDNA detection pipeline for MSK Sequencing Data

  Jupyter Notebook

  •0•0•0•0•Updated Jan 10, 2025Jan 10, 2025

• forte

  Public
  Functional Observation of RNA Transcriptome Elements/Expression

  Nextflow

  •

  MIT License

  •0•7•22•4•Updated Jan 10, 2025Jan 10, 2025

• facetsHeatmap

  Public
  Visualization of copy number profile distributions in a cohort

  R

  •0•0•0•0•Updated Jan 10, 2025Jan 10, 2025

• igo-sample-qc-node

  Public
  Sample QC with nodejs backend

  JavaScript

  •0•0•0•1•Updated Jan 9, 2025Jan 9, 2025

• beagle

  Public
  Voyager Backend

  Python

  •5•2•97•18•Updated Jan 7, 2025Jan 7, 2025

• argos-bam

  Public
  The CWL bam generator for ARGOS, separated into its own repo

  Common Workflow Language

  •0•0•0•0•Updated Jan 7, 2025Jan 7, 2025

• 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 Jan 7, 2025Jan 7, 2025

• igo-delivery

  Public
  Delivery email, symlinks and permissions for IGO projects

  Python

  •

  Apache License 2.0

  •0•0•0•0•Updated Jan 6, 2025Jan 6, 2025

• smile-server

  Public
  Java

  •4•2•74•2•Updated Jan 2, 2025Jan 2, 2025

• smile-databricks-gateway

  Public
  Go

  •

  GNU Affero General Public License v3.0

  •0•0•0•0•Updated Dec 24, 2024Dec 24, 2024

• igo-sample-submission-node

  Public
  Sample Submission API written in node.js

  JavaScript

  •1•0•1•31•Updated Dec 24, 2024Dec 24, 2024

• smile-message-publisher

  Public
  Spring Boot LIMS SampleMetadata publisher framework

  Java

  •

  GNU Affero General Public License v3.0

  •4•0•0•1•Updated Dec 19, 2024Dec 19, 2024

• LimsRest

  Public
  the restful service used by the IGO LIMS

  Java

  •2•2•5•4•Updated Dec 19, 2024Dec 19, 2024

• beagle_cli

  Public
  Beagle API Command Line Utility

  Python

  •1•0•8•3•Updated Dec 19, 2024Dec 19, 2024

• igo-run-qc-node

  Public
  JavaScript

  •0•0•0•0•Updated Dec 18, 2024Dec 18, 2024

• smile-dashboard

  Public
  TypeScript

  •

  GNU Affero General Public License v3.0

  •8•0•0•1•Updated Dec 17, 2024Dec 17, 2024

• tempo

  Public
  CCS research pipeline to process WES and WGS TN pairs

  Groovy

  •5•12•48•9•Updated Dec 13, 2024Dec 13, 2024

• ridgeback

  Public
  Toil API

  Python

  •2•1•38•3•Updated Dec 11, 2024Dec 11, 2024

• facets-preview

  Public
  Load, review and adjust facets fits

  R

  •3•2•4•0•Updated Dec 10, 2024Dec 10, 2024

• igo-genomics

  Public
  Vue

  •0•1•3•0•Updated Dec 10, 2024Dec 10, 2024

• vcf2maf

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

  perlvcfmaf+ 2vepisoforms

  Perl

  •

  Other

  •218•378•89•0•Updated Dec 9, 2024Dec 9, 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 Dec 7, 2024Dec 7, 2024

• smile-label-generator

  Public
  SMILE messaging service for handling CMO label generation

  Java

  •

  GNU Affero General Public License v3.0

  •3•0•0•1•Updated Dec 6, 2024Dec 6, 2024

• neoantigen-pipeline

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

  Python

  •

  MIT License

  •0•1•10•0•Updated Dec 6, 2024Dec 6, 2024

• toil

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

  Python

  •

  Apache License 2.0

  •239•3•0•1•Updated Dec 3, 2024Dec 3, 2024

• argos_report

  Public
  Repository for ARGOS report (v1.0.1 Balto)

  CSS

  •0•0•0•0•Updated Nov 29, 2024Nov 29, 2024

• igo-lims-plugins

  Public
  Sapio LIMS customizations to workflows for IGO

  Java

  •0•2•1•7•Updated Nov 27, 2024Nov 27, 2024

• swabnseq

  Public
  Python

  •0•0•0•0•Updated Nov 26, 2024Nov 26, 2024

• loki

  Public
  Workflow for handling CNV events

  Nextflow

  •

  MIT License

  •1•0•1•0•Updated Nov 25, 2024Nov 25, 2024