Repositories list

• scpca-portal

  Public
  Single-cell Pediatric Cancer Atlas Portal is a growing database of uniformly processed single-cell data from pediatric cancer tumors and model systems

  bioinformaticssingle-cell

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •0•3•54•5•Updated Feb 25, 2025Feb 25, 2025

• scpca-nf

  Public
  scpca-nf is the Nextflow workflow for processing Single-cell Pediatric Cancer Atlas Portal data

  nextflowscrna-seq10xgenomics+ 4spatial-transcriptomicscite-seqrna-seq-quantificationalevin-fry

  R

  •

  BSD 3-Clause "New" or "Revised" License

  •2•13•32•1•Updated Feb 25, 2025Feb 25, 2025

• refinebio-web

  Public
  Refinebio Web

  JavaScript

  •

  BSD 3-Clause "New" or "Revised" License

  •0•1•49•2•Updated Feb 25, 2025Feb 25, 2025

• OpenScPCA-analysis

  Public
  An open, collaborative project to analyze data from the Single-cell Pediatric Cancer Atlas (ScPCA) Portal

  opensciencesingle-cell

  HTML

  •

  Other

  •18•12•31•4•Updated Feb 25, 2025Feb 25, 2025

• scpca-paper-figures

  Public
  Figures for https://github.com/AlexsLemonade/ScPCA-manuscript/

  HTML

  •

  BSD 3-Clause "New" or "Revised" License

  •0•0•10•1•Updated Feb 25, 2025Feb 25, 2025

• OpenScPCA-nf

  Public
  A workflow for running OpenScPCA analysis modules

  R

  •

  BSD 3-Clause "New" or "Revised" License

  •0•0•8•1•Updated Feb 24, 2025Feb 24, 2025

• resources-portal

  Public
  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •1•1•88•5•Updated Feb 20, 2025Feb 20, 2025

• scpca-docs

  Public
  User information about ScPCA processing

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •1•0•13•0•Updated Feb 20, 2025Feb 20, 2025

• medulloblastoma-classifier

  Public
  HTML

  •

  BSD 3-Clause "New" or "Revised" License

  •0•0•18•1•Updated Feb 18, 2025Feb 18, 2025

• 2025-march-training

  Public
  HTML

  •

  Other

  •0•0•8•0•Updated Jan 28, 2025Jan 28, 2025

• refinebio-examples

  Public
  Example workflows for refine.bio data

  gene-expressionpathway-analysisdifferential-expression+ 2notebookbiodata

  HTML

  •

  Other

  •6•11•32•1•Updated Jan 14, 2025Jan 14, 2025

• ScPCA-manuscript

  Public
  The manuscript repository for the Single-cell Pediatric Cancer Atlas (ScPCA)

  HTML

  •

  Creative Commons Attribution 4.0 International

  •1•0•1•0•Updated Jan 14, 2025Jan 14, 2025

• rOpenScPCA

  Public
  R package to support analysis in the OpenScPCA project

  HTML

  •

  Other

  •2•0•7•3•Updated Jan 6, 2025Jan 6, 2025

• training-specific-template

  Public template
  Template repository that can be cloned to create repo for administering a specific training workshop

  HTML

  •

  Other

  •2•0•0•0•Updated Dec 11, 2024Dec 11, 2024

• 2024-december-training

  Public
  HTML

  •

  Other

  •0•0•0•0•Updated Dec 11, 2024Dec 11, 2024

• training-modules

  Public
  A collection of modules that are combined into 1-5 day workshops on computational topics for the childhood cancer research community.

  HTML

  •

  Other

  •29•66•39•0•Updated Dec 9, 2024Dec 9, 2024

• scpcaTools

  Public
  R

  •

  BSD 3-Clause "New" or "Revised" License

  •0•1•12•0•Updated Dec 6, 2024Dec 6, 2024

• refinebio-js

  Public
  Javascript client for refine.bio

  JavaScript

  •

  BSD 3-Clause "New" or "Revised" License

  •0•0•7•8•Updated Nov 20, 2024Nov 20, 2024

• reproducible-research

  Public
  Repository for Reproducible Research Practices Training Workshop

  HTML

  •

  Other

  •3•1•12•0•Updated Oct 18, 2024Oct 18, 2024

• rrp-workshop-exercises

  Public
  Materials for reproducible research practices workshop exercises.

  HTML

  •

  Other

  •43•1•0•0•Updated Sep 19, 2024Sep 19, 2024

• refinebio

  Public
  Refine.bio harmonizes petabytes of publicly available biological data into ready-to-use datasets for cancer researchers and AI/ML scientists.

  Python

  •

  Other

  •20•130•479•14•Updated Sep 3, 2024Sep 3, 2024

• 2024-august-training

  Public
  Website for Data Lab "Introduction to RNA-Seq and Reproducible Research" Training, August 2024 at UMN

  HTML

  •

  Other

  •0•1•0•0•Updated Aug 22, 2024Aug 22, 2024

• refinebio-py

  Public
  A python client for the refine.bio API.

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •3•1•11•2•Updated Aug 21, 2024Aug 21, 2024

• .github

  Public
  1•0•0•0•Updated Jul 18, 2024Jul 18, 2024

• scrumlord

  Public
  Continuous administration of the Greene Lab's electronic scrum

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •8•0•0•0•Updated Jul 16, 2024Jul 16, 2024

• spellcheck

  Public
  This repository contains a Docker image with the R spelling package

  R

  •

  MIT License

  •1•0•1•0•Updated Jun 13, 2024Jun 13, 2024

• 2024-june-training

  Public
  Website for Data Lab "Introduction to Single Cell RNA-Seq" Training, June 2024

  HTML

  •

  Other

  •0•0•0•0•Updated Jun 4, 2024Jun 4, 2024

• alsf-scpca

  Public
  Management and analysis tools for ALSF Single-cell Pediatric Cancer Atlas data.

  HTML

  •

  BSD 3-Clause "New" or "Revised" License

  •1•0•10•0•Updated Apr 5, 2024Apr 5, 2024

• OpenScPCA-manuscript

  Public
  HTML

  •

  Creative Commons Attribution 4.0 International

  •0•0•0•0•Updated Mar 28, 2024Mar 28, 2024

• fancySVD

  Public
  Only the IterativeSVD algorithm from iskandr/fancyimpute to make dependency resolution easier.

  Python

  •

  Apache License 2.0

  •0•1•1•1•Updated Feb 1, 2024Feb 1, 2024