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@oicr-gsi

Genome Sequence Informatics

Repositories for OICR's Genome Sequence Informatics team

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  1. shesmu shesmu Public

    Decision-driven action launching system

    Java 8 3

  2. djerba djerba Public

    Create cancer bioinformatics reports from metadata and workflow output

    Python 7 2

  3. vidarr vidarr Public

    Analysis provenance tracking server

    Java 1 1

  4. data_release data_release Public

    Scripts for releasing data generated at OICR to stakeholders

    Python

Repositories

Showing 10 of 226 repositories
  • 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.

    oicr-gsi/mutect2Consensus’s past year of commit activity
    WDL 0 0 0 2 Updated Jul 2, 2024
  • hrDetect Public

    Workflow for the sigtools and HRdetect R packages

    oicr-gsi/hrDetect’s past year of commit activity
    R 1 1 0 0 Updated Jul 2, 2024
  • probeCoverageDistribution Public

    Workflow to calculate probe coverage, calls bwaMem

    oicr-gsi/probeCoverageDistribution’s past year of commit activity
    WDL 0 GPL-2.0 0 0 0 Updated Jul 2, 2024
  • mavis Public

    MAVIS workflow, annotation of structural variants

    oicr-gsi/mavis’s past year of commit activity
    WDL 0 1 0 0 Updated Jul 2, 2024
  • hotspotFingerprintCollector Public

    common Fingerprint Collector workflow, that aligns sequence and runs 1 or more sample fingerprinting tools

    oicr-gsi/hotspotFingerprintCollector’s past year of commit activity
    WDL 0 0 0 0 Updated Jul 2, 2024
  • nanoporeCoverageAnalysis Public

    Workflow for nanopore coverage analysis, wdl wrapper for snakemake workflow forked from Simpson Lab repo.

    oicr-gsi/nanoporeCoverageAnalysis’s past year of commit activity
    WDL 0 0 0 0 Updated Jul 2, 2024
  • nanoporeMapping Public

    Workflow for nanopore reads mapping, wdl wrapper for snakemake workflow forked from Simpson Lab repo.

    oicr-gsi/nanoporeMapping’s past year of commit activity
    WDL 0 0 0 0 Updated Jul 2, 2024
  • nanoporeRunSVAnalysis Public

    Workflow for running structural variants analysis, wdl wrapper for snakemake workflow forked from Simpson Lab repo.

    oicr-gsi/nanoporeRunSVAnalysis’s past year of commit activity
    WDL 0 0 0 0 Updated Jul 2, 2024
  • nanoporeSVAll Public

    Workflow for executing all task of nanopore filterfastq, nanopore mapping, nanopore coverage analysis, nanopore structural variants analysis, wdl wrapper for snakemake workflow forked from Simpson Lab repo.

    oicr-gsi/nanoporeSVAll’s past year of commit activity
    WDL 0 0 0 0 Updated Jul 2, 2024
  • umiCollapse Public

    umiCollapse workflow, generating umi deduplicated bam file and stats

    oicr-gsi/umiCollapse’s past year of commit activity
    WDL 0 0 0 0 Updated Jul 2, 2024
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