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/malta
Interface and tracking for clinical report generation
oicr-gsi/barcodex-rs
Reimplementation of barcodex for performance
oicr-gsi/guanyin
Reporting repository and report record keeping
oicr-gsi/ncov2019-artic-nf
A Nextflow pipeline for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics), with a focus on ncov2019
oicr-gsi/Analysis_Reports
for generation of analysis reports to accompany released data
oicr-gsi/anonymize_report
A script to anonymize release reports
oicr-gsi/cbioportal_tools
tools for import of data and administration of the gsi cbioportal instance
oicr-gsi/cfMeDIPs-bakeoff-report-infra
Code repo for the OICR bake-off analysis
oicr-gsi/CGI_validation_scripts
scripts for clinical validation of new assays
oicr-gsi/CHORD
A WDL implementation of UMCUGenetics CHORD
oicr-gsi/cnv-analysis
oicr-gsi/drumbeat
A SCORe-compatible server for use on local disk where users upload is unmanaged.
oicr-gsi/epif-gravity
Building software off gravity forms to pull back information about electronic project information forms
oicr-gsi/fastqs_release_tracker
Release information for each run and project for fastqs sequenced at OICR
oicr-gsi/filterVCF
Preprocess VCF for MRDetect and Fragmentomics
oicr-gsi/Gaea
oicr-gsi/illumina-run-dirs
oicr-gsi/immune-tools-public
Tools and scripts for calculating immune activity metrics
oicr-gsi/indelValidate
workflow for indel validation, based on CGI-Tools/6-indelValidate.sh
oicr-gsi/MMRDetect
MMRDetect is a mutational signature-based classifier for identifying tumors with mismatch repair deficiency using whole-genome sequencing data.
oicr-gsi/nanopore-SV-analysis
Structural variant filtering and anlaysis of Nanopore human WGS data.
oicr-gsi/ricoWorkflow
WDL workflow to run the RICO Singularity container
oicr-gsi/sampuru
Answers the question: "where's my sample?"
oicr-gsi/SEXCMD
A fork of SEXCMD repository
oicr-gsi/smmipQCReport
Scripts to generate a summary table with QC metrics for each smMIP libraries
oicr-gsi/somnus
Service inhibitor service
oicr-gsi/svtools
Tools for processing and analyzing structural variants.
oicr-gsi/tape-archiving
Scripts meant to prepare a project for archiving, encrypt it using GPG, verify the output, and then send it to CommVault to write to tape
oicr-gsi/virusdetection
OICR Genomics kraken2 WDL workflow
oicr-gsi/wdlviz
Python tool to create DOT diagrams for WDL workflows