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/miso-lims
MISO: An open-source LIMS for NGS sequencing centres, now with detailed samples
oicr-gsi/arribaToMavis
Convert Arriba output to Mavis format
oicr-gsi/MEDIPS
MEDIPS - MEthylated DNA ImmunoPrecipitation Sequencing analysis
oicr-gsi/ega_tools
oicr-gsi/FusionBenchmarking
Toolkit for benchmarking fusion transcript predictions
oicr-gsi/index-check
oicr-gsi/custom-analysis-pipe
This repo is for some custom analysis pipelines
oicr-gsi/cromwell
Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments
oicr-gsi/bam-qc-metrics
Metrics for BAM file QC
oicr-gsi/longrangerWgs
oicr-gsi/neoantigen-mutation-burden
oicr-gsi/umiExtract
workflow to extract UMI from fastq files and place in fastq header
oicr-gsi/gsi-website
Libraries for making the GSI website
oicr-gsi/gsi-config
Config files for setting up new developers in GSI
oicr-gsi/modelTsne
A t-SNE framework to visualize OMICs data
oicr-gsi/wf_cfmedip-legacy
Workflow for cfMeDIP data analysis using Docker
oicr-gsi/realtimeNanopore
oicr-gsi/platonicdash
Approaches the platonic ideal of a dash application
oicr-gsi/germline-variants-annotation
oicr-gsi/starMulti
oicr-gsi/qc-server-demo
Demonstration of QC web server
oicr-gsi/downsampling-panel-exomes
oicr-gsi/MultiQC
Aggregate results from bioinformatics analyses across many samples into a single report.
oicr-gsi/bamqc-legacy
Perl scripts for generating quality control stats from BAM files
oicr-gsi/xenoclassify
A tool for classifiying short-read sequencing data from xenograft samples.
oicr-gsi/RSeQC-GSI
Fork of the RSeQC Sourceforge repository for RNASeq QC
oicr-gsi/queue_use
Calculate the usage and other stats for an SGE queue
oicr-gsi/miso-lims-docker
Docker container for miso-lims
oicr-gsi/oicr-gsi.github.io
Website for Genome Sequence Informatics
oicr-gsi/miso-docs-oicr
Moved to https://miso-lims.github.io/walkthroughs