Pinned Repositories
dashi
Python Dash visualization of OICR QC data
data_release
Scripts for releasing data generated at OICR to stakeholders
debarcer
Debarcer: A package for De-Barcoding and Error Correction of sequencing data containing molecular barcodes
djerba
Create cancer bioinformatics reports from metadata and workflow output
miso-lims
MISO: An open-source LIMS for NGS sequencing centres, now with detailed samples
modelTsne
A t-SNE framework to visualize OMICs data
robust-paper
Ten Simple Rules for Making Research Software More Robust. Manuscript is published at PLoS Computational Biology. Feedback is welcome!
sequenza
Workflow for Sequenza, cellularity and ploidy
shesmu
Decision-driven action launching system
vidarr
Analysis provenance tracking server
Genome Sequence Informatics's Repositories
oicr-gsi/djerba
Create cancer bioinformatics reports from metadata and workflow output
oicr-gsi/shesmu
Decision-driven action launching system
oicr-gsi/dashi
Python Dash visualization of OICR QC data
oicr-gsi/dimsum
QC Tracking dashboard
oicr-gsi/pinery
A LIMS abstraction layer to provide generalized LIMS access via a web service.
oicr-gsi/purple
oicr-gsi/vidarr
Analysis provenance tracking server
oicr-gsi/cardea
Case data API
oicr-gsi/cerberus
File provenance library
oicr-gsi/data_release
Scripts for releasing data generated at OICR to stakeholders
oicr-gsi/bamToFastq
Generate R1 and R2
oicr-gsi/bclconvert
Workflow to process a run directory through Dragen bclconvert
oicr-gsi/biomodalQC
QC workflow for biomodal pipeline
oicr-gsi/callability
oicr-gsi/crosscheck_fingerprint_caller
To call sequencing library swaps and matches from CrosscheckFingerprints output given OICR metadata
oicr-gsi/crosscheckFingerprintCaller
To call sequencing library swaps and matches from CrosscheckFingerprints output given OICR metadata
oicr-gsi/Dragen-somatic
The Dragen somatic variant calling workflow
oicr-gsi/flask_ui
projectconfig UI
oicr-gsi/Gaea
Register genomics data in EGA
oicr-gsi/illumina-run-dirs
oicr-gsi/mrdetect
workflow to detect Minimal Residual disease with MRDetect
oicr-gsi/mutect2Consensus
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/nabu
QC tracking for files via a web service
oicr-gsi/Nextflow_WG_pipeline
oicr-gsi/optitype
Workflow for HLA genotyping prediction with optitype
oicr-gsi/pinery-reports
Reports based on data from Pinery
oicr-gsi/provenanceReporter
oicr-gsi/sampuru
Answers the question: "where's my sample?"
oicr-gsi/smmipQC
Set up manual smMip QC analyses
oicr-gsi/smmipQCReport
Scripts to generate a summary table with QC metrics for each smMIP libraries