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
medips-tools
Scripts for cfMeDIP QC analysis
miso-lims
MISO: An open-source LIMS for NGS sequencing centres, now with detailed samples
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/emSeqQc
Runs bwa-meth followed by bamqc and methyldackel
oicr-gsi/estimate
ESTIMATE provides researchers with scores for tumor purity, the level of stromal cells present, and the infiltration level of immune cells in tumor tissues based on expression data
oicr-gsi/hrDetect
Workflow for the sigtools and HRdetect R packages
oicr-gsi/sample-fingerprinting
workflow that generates genotype fingerprints consumed by SampleFingerprinting workflow
oicr-gsi/bcl2barcode
oicr-gsi/calculateContamination
A WDL workflow that runs GATK4 CalculateContamination from FastQ files.
oicr-gsi/consensusCruncherWorkflow
A workflow which combines consensus cruncher and mutect2
oicr-gsi/dellyGermline
Call germline SVs using Delly
oicr-gsi/dragmap
A workflow to run Dragmap
oicr-gsi/gatk-genotype-GVCFs
Genotype GVCFs WDL workflow for GATK4
oicr-gsi/hotspotFingerprintCollector
common Fingerprint Collector workflow, that aligns sequence and runs 1 or more sample fingerprinting tools
oicr-gsi/mavis
MAVIS workflow, annotation of structural variants
oicr-gsi/mavis3
MAVIS workflow, annotation of structural variants
oicr-gsi/minimap2
Workflow to align long read fastq files to a reference genome
oicr-gsi/msisensor
msisensor-pro workflow
oicr-gsi/nanoporeCoverageAnalysis
Workflow for nanopore coverage analysis, wdl wrapper for snakemake workflow forked from Simpson Lab repo.
oicr-gsi/nanoporeFilterFastq
Workflow for filter nanopore fastq file, wdl wrapper for snakemake workflow forked from Simpson Lab repo.
oicr-gsi/nanoporeMapping
Workflow for nanopore reads mapping, wdl wrapper for snakemake workflow forked from Simpson Lab repo.
oicr-gsi/nanoporeRunSVAnalysis
Workflow for running structural variants analysis, wdl wrapper for snakemake workflow forked from Simpson Lab repo.
oicr-gsi/nanoporeSVAll
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/ncov2019ArticNf
ncov2019ArticNf workflow executes the ncov2019-artic-nf Nextflow workflow from connor-lab (https://github.com/connor-lab/ncov2019-artic-nf).
oicr-gsi/probeCoverageDistribution
Workflow to calculate probe coverage, calls bwaMem
oicr-gsi/rsem
WDL workflow for RSEM tool (transcription analysis for RNAseq)
oicr-gsi/smallBamQc
Generate BAM file metrics for OICR's QC Gates as fast as possible
oicr-gsi/sniffles
Workflow to run Structural Variant caller for Nanopore
oicr-gsi/star
Workflow for STAR RNAseq aligner
oicr-gsi/t1k
oicr-gsi/tmbAnalysis
A workflow to align fastq reads, call variants, annotate and assess TMB
oicr-gsi/umiCollapse
umiCollapse workflow, generating umi deduplicated bam file and stats
oicr-gsi/variantMerging
a workflow for combining variant calls from SNV analyses done with different callers