oicr-gsi/queue_use

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1
Language
Python
License
MIT License
Created over 7 years ago
Updated over 5 years ago

oicr-gsi/queue_use

oicr-gsi

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Calculate the usage and other stats for an SGE queue

debarcer

Debarcer: A package for De-Barcoding and Error Correction of sequencing data containing molecular barcodes

robust-paper

Ten Simple Rules for Making Research Software More Robust. Manuscript is published at PLoS Computational Biology. Feedback is welcome!

djerba

Create cancer bioinformatics reports from metadata and workflow output

shesmu

Decision-driven action launching system

sequenza

Workflow for Sequenza, cellularity and ploidy

dashi

Python Dash visualization of OICR QC data

variantEffectPredictor

Variant Effect Predictor Workflow

cfMedipsQc

cfMedipsQC workflow produces a set of metrics files for sequencing data generated in methylation profiling of circulating Free DNA.

medips-tools

Scripts for cfMeDIP QC analysis

hmmcopy

Calls Copy Number Variants on sequencing data from cancer patients

wf_cfmedip

Workflow for cfMeDIP data analysis using Docker

emSeqQc

Runs bwa-meth followed by bamqc and methyldackel

arriba

Fusion caller which runs off of STAR bam

malta

Interface and tracking for clinical report generation

xenoclassify

A tool for classifiying short-read sequencing data from xenograft samples.

modelTsne

A t-SNE framework to visualize OMICs data

strelkaSomatic

Strelka2 somatic variant calling workflow

hrDetect

Workflow for the sigtools and HRdetect R packages

dimsum

QC Tracking dashboard

ercc

workflow for analysis of samples with RNA spike-ins (ERCC)

barcodex-rs

Reimplementation of barcodex for performance

hlaminer

wrapper workflow for BCGSC tool HLAminer

sexcmdWorkflow

wdl wrapper for SEXCMD tool. Identification of donor's sex using fastq inputs

vidarr

Analysis provenance tracking server

pinery

A LIMS abstraction layer to provide generalized LIMS access via a web service.

delly

Delly workflow produces a set of vcf files with different types of structural variant calls

miso-lims-docker

Docker container for miso-lims

gsi-ontologies

bamQC

Workflow to run bam-qc-metrics (https://github.com/oicr-gsi/bam-qc-metrics)

mutect2

Workflow to run Mutect2 (GATK4)

illumina-report

umiConsensus

Workflow to generate consensus sequence bases on UMIs using consensusCruncher.

guanyin

Reporting repository and report record keeping

haplotypeCaller

Haplotype caller WDL workflow for GATK4

gsi-wdl-tools

rnaSeqQC

RNASeqQC workflow

crosscheckFingerprintsCollector

workflow to generate per library fingerprints for use in gatk CrosscheckFingerprints

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

gridss

OICR WDL implementation of GRIDSS PURPLE LINX

purple