stjudecloud repositories

32 repositories

workflows
Public
Bioinformatics workflows developed for and used on the St. Jude Cloud project.
workflow bioinformatics genomics
workflow bioinformatics genomics workflow-engine computational-biology next-generation-sequencing wdl cwl workflows cromwell
WDL
•
MIT License
•15•45•11•7•Updated Oct 8, 2026Oct 8, 2026
docs
Public
Educational materials for the St. Jude Cloud project.
TypeScript
•
MIT License
•1•2•7•24•Updated Oct 7, 2026Oct 7, 2026
ngsderive
Public
Forensic analysis tool useful in backwards computing information from next-generation sequencing data.
workflow bioinformatics genomics
workflow bioinformatics genomics workflow-engine ngs computational-biology next-generation-sequencing strandedness strandedness-inference gene-model
Python
•
MIT License
•0•11•0•5•Updated Sep 7, 2026Sep 7, 2026
expression-classification
Public
Python
•
MIT License
•0•2•1•2•Updated Aug 5, 2026Aug 5, 2026
ecc
Public
The Encyclopedia of Composable Characteristics (ECC).
Rust
•
Apache License 2.0
•0•3•3•4•Updated Jul 16, 2026Jul 16, 2026
cde-transformers
Public
A PHP package to transform values into caDSR CDEs permissible values to be used for the CCDI API.
PHP
•
Other
•0•0•0•2•Updated Feb 17, 2026Feb 17, 2026
cgc-go
Public
Go
•0•0•0•1•Updated Dec 5, 2025Dec 5, 2025
wdldoc
Public archive
Create WDL documentation using Markdown.
workflow bioinformatics genomics
workflow bioinformatics genomics computational-biology next-generation-sequencing wdl cromwell wdl-workflow stjudecloud
Python
•
MIT License
•5•29•0•2•Updated Nov 25, 2025Nov 25, 2025
dx-rnaseq_standard
Public
Monolithic DNAnexus implementation of RNA-Seq V2 pipeline with miniwdl
Shell
•0•0•0•1•Updated Mar 7, 2025Mar 7, 2025
university
Public archive
Educational materials for the St. Jude Cloud project.
JavaScript
•23•4•0•12•Updated Jan 27, 2025Jan 27, 2025
rfcs
Public
Request for Comments (RFCs) on the St. Jude Cloud Project.
discussion workflow bioinformatics
discussion workflow bioinformatics genomics proposal workflow-engine computational-biology bioinformatics-pipeline wdl cwl
Jupyter Notebook
•2•1•0•4•Updated Jan 13, 2025Jan 13, 2025
ontology
Public
Documentation related to the ontology initiative.
0•0•0•0•Updated Nov 21, 2024Nov 21, 2024
dapr-php-sdk
Public
Dapr SDK for PHP
PHP
•
Apache License 2.0
•19•0•0•4•Updated Nov 12, 2024Nov 12, 2024
msgenctl
Public archive
CLI to manage Microsoft Genomics workflows
Go
•
MIT License
•0•0•0•0•Updated Oct 28, 2024Oct 28, 2024
theme
Public
Component library and CSS themes for applications on the St. Jude Cloud project.
react css sass
react css sass theme bootstrap fonts vue tailwindcss stjudecloud
Handlebars
•3•1•0•30•Updated Aug 28, 2024Aug 28, 2024
utilities
Public
Utility scripts created for and used on the St. Jude Cloud team.
Python
•
MIT License
•0•0•0•5•Updated Apr 29, 2024Apr 29, 2024
merge-counts
Public
Utility for merging RNA-seq expression counts files from St. Jude Cloud.
Python
•
MIT License
•1•1•0•5•Updated Oct 10, 2023Oct 10, 2023
mkdocs-stjudecloud
Public
A Material Design theme for MkDocs
HTML
•
MIT License
•4.1k•0•0•4•Updated Jul 20, 2023Jul 20, 2023
mtsg
Public
Find and quantify COSMIC mutational signatures across samples
Python
•
MIT License
•1•2•0•1•Updated Jul 6, 2023Jul 6, 2023
bioinformatics-tool-template
Public template
Dockerfile
•
MIT License
•1•2•0•0•Updated Mar 27, 2023Mar 27, 2023
dx-rapid_rnaseq
Public
0•0•0•0•Updated Sep 6, 2022Sep 6, 2022
dx-tag_outputs
Public
Python
•
MIT License
•0•0•0•0•Updated Aug 30, 2022Aug 30, 2022
dx-build_visualizer
Public
Python
•
MIT License
•0•0•0•0•Updated Aug 30, 2022Aug 30, 2022
dx-fuzzion
Public
DNAnexus implementation of Fuzzion (https://github.com/stjude/fuzzion)
Shell
•0•0•0•1•Updated Aug 30, 2022Aug 30, 2022
dx-coverage_bw
Public
Java
•0•0•0•0•Updated Aug 30, 2022Aug 30, 2022
dx-STAR
Public
DNAnexus app wrapper for STAR alignment
Python
•
MIT License
•0•0•0•0•Updated Aug 30, 2022Aug 30, 2022
release-python-action
Public
Github Action to release a Poetry-based Python app as we regularly do on the St. Jude Cloud project.
MIT License
•0•0•0•0•Updated Aug 30, 2022Aug 30, 2022
dx-rnapeg
Public archive
Perl
•0•0•0•1•Updated May 17, 2022May 17, 2022
docs-archive
Public archive
Documentation on St. Jude Cloud.
documentation bioinformatics computational-biology
documentation bioinformatics computational-biology next-generation-sequencing bioinformatics-pipeline stjudecloud
Shell
•
MIT License
•6•7•1•4•Updated Apr 28, 2022Apr 28, 2022
dx-manta
Public
Shell
•0•0•0•0•Updated Jan 29, 2021Jan 29, 2021

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St. Jude Cloud

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32 repositories

workflows

docs

ngsderive

expression-classification

ecc

cde-transformers

cgc-go

wdldoc

dx-rnaseq_standard

university

rfcs

ontology

dapr-php-sdk

msgenctl

theme

utilities

merge-counts

mkdocs-stjudecloud

mtsg

bioinformatics-tool-template

dx-rapid_rnaseq

dx-tag_outputs

dx-build_visualizer

dx-fuzzion

dx-coverage_bw

dx-STAR

release-python-action

dx-rnapeg

docs-archive

dx-manta

Repositories list

32 repositories