Genomic Data Commons

All

84 repositories

indexd
Public
Index service server
backend core
Python
•
Apache License 2.0
•20•3•0•10•Updated Jan 28, 2025Jan 28, 2025
gdc-rnaseq-tool
Public
Utility scripts for RNA-seq workflows
docker bioinformatics workflow-tool
Python
•
Apache License 2.0
•1•1•1•2•Updated Jan 28, 2025Jan 28, 2025
bio_qcmetrics_tool
Public
Framework for serializing QC metrics into different formats for bioinformatics workflows
docker bioinformatics workflow-tool
Python
•
Apache License 2.0
•0•0•0•1•Updated Jan 28, 2025Jan 28, 2025
bio-tarball-to-fastqgz
Public
Tool to extract fastq files from complicated tarballs and provide them as standard gzipped fastq files with metadata as json.
Python
•
Apache License 2.0
•0•0•0•3•Updated Jan 28, 2025Jan 28, 2025
gdc-rnaseq-cwl
Public
GDC RNA-Seq STAR 2-Pass Workflow
workflow bioinformatics cwl
Common Workflow Language
•
Apache License 2.0
•8•2•0•3•Updated Jan 28, 2025Jan 28, 2025
bam_readgroup_to_json
Public
Extract a readgroup from a BAM, and write it as json
docker bioinformatics workflow-tool
Python
•
Apache License 2.0
•3•0•0•5•Updated Jan 28, 2025Jan 28, 2025
fastqc-docker
Public
docker bioinformatics
Shell
•
Apache License 2.0
•0•0•0•0•Updated Jan 28, 2025Jan 28, 2025
gdc-frontend-framework
Public
TypeScript
•
Apache License 2.0
•0•10•0•9•Updated Jan 27, 2025Jan 27, 2025
gdc-docs
Public
Official repository for GDC User Guides in Markdown format
JavaScript
•
Apache License 2.0
•45•60•0•17•Updated Jan 24, 2025Jan 24, 2025
aliquot-maf-cwl
Public
CWL tools and workflows for generating and processing aliquot-MAF
workflow bioinformatics maf-files cwl
Common Workflow Language
•
Apache License 2.0
•2•0•0•1•Updated Jan 22, 2025Jan 22, 2025
aliquot-maf-tools
Public
Tools for creating and filtering aliquot-level MAFs
docker bioinformatics maf-files workflow-tool
Python
•
Apache License 2.0
•2•5•0•0•Updated Jan 22, 2025Jan 22, 2025
gdc-sanger-somatic-tool
Public
Support scripts for the sanger somatic workflows
docker bioinformatics workflow-tool
Python
•
Apache License 2.0
•1•0•0•2•Updated Jan 16, 2025Jan 16, 2025
gdc-models
Public
Git repository centrally stores and serves GDC data models defined in static YAML files
library core
Python
•1•3•4•1•Updated Dec 24, 2024Dec 24, 2024
variant-filtration-cwl
Public
Workflows for filtering GDC VCFs
workflow bioinformatics cwl
Common Workflow Language
•
Apache License 2.0
•2•1•0•0•Updated Dec 20, 2024Dec 20, 2024
psqlgraph
Public
Library for graph-like storage in postgresql using sqlalchemy
library core
Python
•
Apache License 2.0
•6•22•5•4•Updated Dec 19, 2024Dec 19, 2024
gdc-ng-models
Public
library core
Python
•
Apache License 2.0
•1•2•0•2•Updated Dec 17, 2024Dec 17, 2024
survivalplot
Public
JavaScript
•4•0•0•8•Updated Dec 12, 2024Dec 12, 2024
boxplot
Public
JavaScript
•1•0•0•9•Updated Dec 12, 2024Dec 12, 2024
bio-colors
Public
JavaScript
•
Apache License 2.0
•1•0•0•2•Updated Dec 12, 2024Dec 12, 2024
qqplot
Public
JavaScript
•1•0•0•10•Updated Dec 12, 2024Dec 12, 2024
webdev_wfui-react
Public
UI library used by the main GDC site
JavaScript
•1•0•0•5•Updated Dec 12, 2024Dec 12, 2024
variant-filtration-tool
Public
Support tools for the GDC Variant Filtration Workflow
docker bioinformatics workflow-tool
Python
•
Apache License 2.0
•2•1•0•3•Updated Sep 30, 2024Sep 30, 2024
gdcdictionary
Public
Data dictionary for the GDC
library core
Python
•
Apache License 2.0
•37•50•4•8•Updated Sep 17, 2024Sep 17, 2024
indexclient
Public
Prototype index service client.
library core
Python
•
Apache License 2.0
•2•0•0•1•Updated Sep 12, 2024Sep 12, 2024
gdc-client
Public
GDC Data Transfer Tool
Python
•
Apache License 2.0
•40•147•19•29•Updated Sep 11, 2024Sep 11, 2024
cdisutils
Public
Utility modules for GDC functionality
library core
Python
•2•1•0•14•Updated Aug 12, 2024Aug 12, 2024
gatk4_mutect2_cwl
Public
workflow bioinformatics cwl
Common Workflow Language
•
Apache License 2.0
•0•0•0•0•Updated Aug 7, 2024Aug 7, 2024
samtools-mpileup-tool
Public
GDC samtools mpileup tool docker
docker bioinformatics workflow-tool
Python
•
Apache License 2.0
•1•0•0•1•Updated Aug 6, 2024Aug 6, 2024
samtools-mpileup-cwl
Public
CWL for GDC samtools mpileup
workflow bioinformatics cwl
Common Workflow Language
•
Apache License 2.0
•1•0•0•0•Updated Aug 5, 2024Aug 5, 2024
gdc-dnaseq-cwl
Public
CWL for GDC DNASeq workflows
bioinformatics workflow cwl
Common Workflow Language
•
Apache License 2.0
•14•22•0•2•Updated Jul 18, 2024Jul 18, 2024