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/dashi
Python Dash visualization of OICR QC data
oicr-gsi/medips-tools
Scripts for cfMeDIP QC analysis
oicr-gsi/ConsensusCruncher
ConsensusCruncher is a tool that suppresses errors in next-generation sequencing data by using unique molecular identifers (UMIs) to amalgamate reads derived from the same DNA template into a consensus sequence.
oicr-gsi/ercc
workflow for analysis of samples with RNA spike-ins (ERCC)
oicr-gsi/gsi-wdl-tools
oicr-gsi/pinery
A LIMS abstraction layer to provide generalized LIMS access via a web service.
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/workflowTracker
workflow tracker, collect and present information for Production Workflows
oicr-gsi/ace
Absolute Copy number Estimation using low-coverage whole genome sequencing data
oicr-gsi/analysisProcedures
oicr-gsi/bamToFastq
Generate R1 and R2
oicr-gsi/bis-utils
This repo contains scripts that are routinely used for BIS team
oicr-gsi/cramConverter
a workflow to run bamToCram or cramToBam
oicr-gsi/crosscheckFingerprints
oicr-gsi/dnaSeqQC
DNASeqQC Pipeline; chains bwaMem, fastQC, and bamQC
oicr-gsi/Dragen-Align
Lane Level (single fastq pair) alignments using Dragen
oicr-gsi/Dragen-somatic
The Dragen somatic variant calling workflow
oicr-gsi/flask_ui
projectconfig UI
oicr-gsi/fragment-score
A computational method that detects cancer in a blood sample.
oicr-gsi/hisat2
Workflow for hisat2, a graph-based aligner
oicr-gsi/injectFastq
Check and inject fastq files
oicr-gsi/nabu
QC tracking for files via a web service
oicr-gsi/pinery-reports
Reports based on data from Pinery
oicr-gsi/provenance
A Java API for LIMS and analysis metadata
oicr-gsi/provenanceReporter
oicr-gsi/smmipQC
Set up manual smMip QC analyses
oicr-gsi/swap_caller
oicr-gsi/vidarr-tools
The home of Python tools for use with Víðarr