oicr-gsi/hmmcopy oicr-gsi/hmmcopy

  • Stars
    star
    3
  • Rank 3,949,427 (Top 79 %)
  • Language WDL
  • Created over 3 years ago
  • Updated 3 months ago
Twitter logo Share LinkedIn logo Share Facebook logo Share
oicr-gsi/hmmcopy
github

oicr-gsi

Reviews

There are no reviews yet. Be the first to send feedback to the community and the maintainers!

Repository Details

Calls Copy Number Variants on sequencing data from cancer patients

More Repositories

1

debarcer

Debarcer: A package for De-Barcoding and Error Correction of sequencing data containing molecular barcodes
Python
13
star
2

robust-paper

Ten Simple Rules for Making Research Software More Robust. Manuscript is published at PLoS Computational Biology. Feedback is welcome!
TeX
11
star
3

djerba

Create cancer bioinformatics reports from metadata and workflow output
Python
8
star
4

shesmu

Decision-driven action launching system
Java
7
star
5

sequenza

Workflow for Sequenza, cellularity and ploidy
R
7
star
6

dashi

Python Dash visualization of OICR QC data
Python
4
star
7

variantEffectPredictor

Variant Effect Predictor Workflow
WDL
3
star
8

cfMedipsQc

cfMedipsQC workflow produces a set of metrics files for sequencing data generated in methylation profiling of circulating Free DNA.
WDL
3
star
9

medips-tools

Scripts for cfMeDIP QC analysis
R
3
star
10

wf_cfmedip

Workflow for cfMeDIP data analysis using Docker
WDL
2
star
11

emSeqQc

Runs bwa-meth followed by bamqc and methyldackel
WDL
2
star
12

arriba

Fusion caller which runs off of STAR bam
WDL
2
star
13

malta

Interface and tracking for clinical report generation
Python
2
star
14

xenoclassify

A tool for classifiying short-read sequencing data from xenograft samples.
Python
2
star
15

modelTsne

A t-SNE framework to visualize OMICs data
R
2
star
16

strelkaSomatic

Strelka2 somatic variant calling workflow
WDL
1
star
17

hrDetect

Workflow for the sigtools and HRdetect R packages
R
1
star
18

dimsum

QC Tracking dashboard
Java
1
star
19

ercc

workflow for analysis of samples with RNA spike-ins (ERCC)
WDL
1
star
20

barcodex-rs

Reimplementation of barcodex for performance
Rust
1
star
21

hlaminer

wrapper workflow for BCGSC tool HLAminer
WDL
1
star
22

sexcmdWorkflow

wdl wrapper for SEXCMD tool. Identification of donor's sex using fastq inputs
WDL
1
star
23

vidarr

Analysis provenance tracking server
Java
1
star
24

pinery

A LIMS abstraction layer to provide generalized LIMS access via a web service.
Java
1
star
25

delly

Delly workflow produces a set of vcf files with different types of structural variant calls
WDL
1
star
26

miso-lims-docker

Docker container for miso-lims
Dockerfile
1
star
27

gsi-ontologies

1
star
28

bamQC

Workflow to run bam-qc-metrics (https://github.com/oicr-gsi/bam-qc-metrics)
WDL
1
star
29

mutect2

Workflow to run Mutect2 (GATK4)
WDL
1
star
30

illumina-report

JavaScript
1
star
31

umiConsensus

Workflow to generate consensus sequence bases on UMIs using consensusCruncher.
WDL
1
star
32

guanyin

Reporting repository and report record keeping
JavaScript
1
star
33

haplotypeCaller

Haplotype caller WDL workflow for GATK4
WDL
1
star
34

gsi-wdl-tools

Python
1
star
35

rnaSeqQC

RNASeqQC workflow
WDL
1
star
36

crosscheckFingerprintsCollector

workflow to generate per library fingerprints for use in gatk CrosscheckFingerprints
WDL
1
star
37

queue_use

Calculate the usage and other stats for an SGE queue
Python
1
star
38

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
Java
1
star
39

gridss

OICR WDL implementation of GRIDSS PURPLE LINX
WDL
1
star
40

purple

WDL
1
star