Repositories list

• workflows

  Public
  Bioinformatics workflows developed for and used on the St. Jude Cloud project.

  workflowbioinformaticsgenomics+ 11workflow-enginecomputational-biologynext-generation-sequencingwdlcwlworkflowscromwell+ 4

  WDL

  •

  MIT License

  •10•34•15•4•Updated Jan 31, 2025Jan 31, 2025

• cde-transformers

  Public
  TODO

  PHP

  •

  Other

  •0•0•0•1•Updated Jan 30, 2025Jan 30, 2025

• university

  Public
  Educational materials for the St. Jude Cloud project.

  JavaScript

  •23•4•0•12•Updated Jan 27, 2025Jan 27, 2025

• wdldoc

  Public
  Create WDL documentation using Markdown.

  workflowbioinformaticsgenomics+ 6computational-biologynext-generation-sequencingwdlcromwellwdl-workflowstjudecloud

  Python

  •

  MIT License

  •5•27•0•3•Updated Jan 27, 2025Jan 27, 2025

• ngsderive

  Public
  Forensic analysis tool useful in backwards computing information from next-generation sequencing data.

  workflowbioinformaticsgenomics+ 7workflow-enginecomputational-biologynext-generation-sequencingngsstrandednessstrandedness-inferencegene-model

  Python

  •

  MIT License

  •0•11•0•2•Updated Jan 27, 2025Jan 27, 2025

• ecc

  Public
  The Encyclopedia of Composable Characteristics (ECC).

  Rust

  •

  Apache License 2.0

  •0•3•2•2•Updated Jan 17, 2025Jan 17, 2025

• rfcs

  Public
  Request for Comments (RFCs) on the St. Jude Cloud Project.

  workflowbioinformaticsgenomics+ 11workflow-enginecomputational-biologybioinformatics-pipelinewdlcwlwdl-workflowcwl-workflow+ 4

  Jupyter Notebook

  •2•0•0•7•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

  •16•0•0•4•Updated Nov 12, 2024Nov 12, 2024

• msgenctl

  Public
  CLI to manage Microsoft Genomics workflows

  Go

  •

  MIT License

  •0•0•0•0•Updated Oct 28, 2024Oct 28, 2024

• expression-classification

  Public
  Python

  •

  MIT License

  •0•2•2•1•Updated Sep 25, 2024Sep 25, 2024

• theme

  Public
  Component library and CSS themes for applications on the St. Jude Cloud project.

  reactsasstheme+ 6bootstrapfontsvuetailwindcssstjudecloudcss

  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

• dx-rnaseq_standard

  Public
  Monolithic DNAnexus implementation of RNA-Seq V2 pipeline with miniwdl

  Shell

  •0•0•0•0•Updated Feb 9, 2024Feb 9, 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

  •3.6k•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.

  documentationbioinformaticscomputational-biology+ 3next-generation-sequencingbioinformatics-pipelinestjudecloud

  Shell

  •

  MIT License

  •6•7•1•4•Updated Apr 28, 2022Apr 28, 2022

• cgc-go

  Public
  Go

  •0•0•0•0•Updated Jul 12, 2021Jul 12, 2021

• dx-manta

  Public
  Shell

  •0•0•0•0•Updated Jan 29, 2021Jan 29, 2021

• stjude_htseq_count

  Public
  Shell

  •0•0•0•0•Updated Dec 8, 2020Dec 8, 2020