Repositories list

• djerba

  Public
  Create cancer bioinformatics reports from metadata and workflow output

  infrastructureinterpretation

  Python

  •

  GNU General Public License v3.0

  •4•9•5•5•Updated Dec 12, 2024Dec 12, 2024

• Gaea

  Public
  Register genomics data in EGA

  toolsrelease

  Python

  •

  MIT License

  •0•0•2•0•Updated Dec 12, 2024Dec 12, 2024

• kallisto

  Public
  Quantifying abundances of transcripts from RNA-Seq data

  0•0•0•1•Updated Dec 11, 2024Dec 11, 2024

• dimsum

  Public
  QC Tracking dashboard

  infrastructure

  Java

  •

  GNU General Public License v3.0

  •0•1•0•2•Updated Dec 11, 2024Dec 11, 2024

• mutect2Consensus

  Public
  The Mutect2Consensus workflow will process umiConsensus outputs for the tumour data through mutect2 in tumour only mode to call variants then use information from the matched normal to identify likely germline variants.

  workflow

  WDL

  •0•0•0•0•Updated Dec 11, 2024Dec 11, 2024

• optitype

  Public
  Workflow for HLA genotyping prediction with optitype

  WDL

  •0•0•0•1•Updated Dec 11, 2024Dec 11, 2024

• msisensor

  Public
  msisensor-pro workflow

  workflow

  WDL

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

• cardea

  Public
  Case data API

  infrastructure

  Java

  •

  Apache License 2.0

  •0•0•0•1•Updated Dec 9, 2024Dec 9, 2024

• vidarr

  Public
  Analysis provenance tracking server

  infrastructure

  Java

  •

  MIT License

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

• nabu

  Public
  QC tracking for files via a web service

  infrastructure

  JavaScript

  •

  MIT License

  •0•0•2•0•Updated Dec 6, 2024Dec 6, 2024

• sampuru

  Public
  Answers the question: "where's my sample?"

  infrastructure

  Java

  •0•0•0•2•Updated Dec 6, 2024Dec 6, 2024

• data_release

  Public
  Scripts for releasing data generated at OICR to stakeholders

  infrastructureanalysis

  Python

  •

  MIT License

  •0•0•0•0•Updated Dec 3, 2024Dec 3, 2024

• crosscheck_fingerprint_caller

  Public
  To call sequencing library swaps and matches from CrosscheckFingerprints output given OICR metadata

  Python

  •0•0•0•0•Updated Nov 28, 2024Nov 28, 2024

• shesmu

  Public
  Decision-driven action launching system

  infrastructurebioinformaticsbioinformatics-pipeline+ 2workflow-managementworkflow-launching

  Java

  •

  MIT License

  •4•8•0•1•Updated Nov 28, 2024Nov 28, 2024

• crosscheckFingerprintCaller

  Public
  To call sequencing library swaps and matches from CrosscheckFingerprints output given OICR metadata

  WDL

  •0•0•0•0•Updated Nov 28, 2024Nov 28, 2024

• Dragen-somatic

  Public
  The Dragen somatic variant calling workflow

  workflow

  WDL

  •0•0•0•0•Updated Nov 27, 2024Nov 27, 2024

• smmipQCReport

  Public
  Scripts to generate a summary table with QC metrics for each smMIP libraries

  toolsanalysis

  Python

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

• bamToFastq

  Public
  Generate R1 and R2

  workflow

  WDL

  •0•0•0•0•Updated Nov 21, 2024Nov 21, 2024

• flask_ui

  Public
  projectconfig UI

  toolspipeline

  Python

  •

  MIT License

  •0•0•0•0•Updated Nov 21, 2024Nov 21, 2024

• pinery

  Public
  A LIMS abstraction layer to provide generalized LIMS access via a web service.

  infrastructure

  Java

  •

  GNU General Public License v3.0

  •0•1•0•0•Updated Nov 20, 2024Nov 20, 2024

• illumina-run-dirs

  Public
  toolsdata-management

  Perl

  •

  MIT License

  •0•0•1•0•Updated Nov 19, 2024Nov 19, 2024

• cerberus

  Public
  File provenance library

  infrastructure

  Java

  •

  MIT License

  •0•0•0•1•Updated Nov 19, 2024Nov 19, 2024

• mrdetect

  Public
  workflow to detect Minimal Residual disease with MRDetect

  workflow

  WDL

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

• biomodalQC

  Public
  QC workflow for biomodal pipeline

  WDL

  •0•0•0•0•Updated Nov 7, 2024Nov 7, 2024

• callability

  Public
  workflow

  WDL

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

• smmipQC

  Public
  Set up manual smMip QC analyses

  workflow

  Python

  •0•0•0•0•Updated Oct 30, 2024Oct 30, 2024

• dashi

  Public
  Python Dash visualization of OICR QC data

  infrastructureqc

  Python

  •

  MIT License

  •2•4•0•1•Updated Oct 18, 2024Oct 18, 2024

• bclconvert

  Public
  Workflow to process a run directory through Dragen bclconvert

  workflow

  WDL

  •0•0•0•0•Updated Oct 17, 2024Oct 17, 2024

• Nextflow_WG_pipeline

  Public
  workflow

  Nextflow

  •0•0•0•0•Updated Oct 3, 2024Oct 3, 2024

• provenanceReporter

  Public
  infrastructureanalysis

  Python

  •0•0•0•0•Updated Sep 27, 2024Sep 27, 2024