Repositories list

• scpcaTools

  Public
  R

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

  •0•1•12•2•Updated Aug 1, 2025Aug 1, 2025

• 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

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

  •0•4•73•5•Updated Aug 1, 2025Aug 1, 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

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

  •2•14•47•1•Updated Aug 1, 2025Aug 1, 2025

• OpenScPCA-analysis

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

  opensciencesingle-cell

  HTML

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  Other

  •22•14•42•3•Updated Aug 1, 2025Aug 1, 2025

• 2025-august-training

  Public
  HTML

  •

  Other

  •0•0•0•0•Updated Jul 31, 2025Jul 31, 2025

• OpenScPCA-nf

  Public
  A workflow for running OpenScPCA analysis modules

  R

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

  •0•1•8•0•Updated Jul 30, 2025Jul 30, 2025

• scpca-docs

  Public
  User information about ScPCA processing

  Python

  •

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

  •1•0•15•0•Updated Jul 25, 2025Jul 25, 2025

• medulloblastoma-classifier

  Public
  HTML

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

  •0•0•17•1•Updated Jul 21, 2025Jul 21, 2025

• 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

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  Other

  •31•70•32•0•Updated Jul 17, 2025Jul 17, 2025

• rOpenScPCA

  Public
  R package to support analysis in the OpenScPCA project

  HTML

  •

  Other

  •2•0•7•2•Updated Jul 7, 2025Jul 7, 2025

• 2025-june-training

  Public
  HTML

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  Other

  •0•0•0•0•Updated Jun 9, 2025Jun 9, 2025

• alsf-scpca

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

  HTML

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

  •1•0•6•0•Updated Jun 3, 2025Jun 3, 2025

• refinebio-web

  Public
  Refinebio Web

  JavaScript

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

  •0•1•34•0•Updated May 29, 2025May 29, 2025

• ScPCA-manuscript

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

  HTML

  •

  Creative Commons Attribution 4.0 International

  •1•0•4•0•Updated May 29, 2025May 29, 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•1•0•Updated May 22, 2025May 22, 2025

• scpca-paper-figures

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

  HTML

  •

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

  •0•0•4•0•Updated May 19, 2025May 19, 2025

• 2025-treehouse-training

  Public
  Reproducible Research Practices and Code Review Workshop for UCSC Treehouse Childhood Cancer Initiative

  Shell

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  Creative Commons Attribution 4.0 International

  •0•0•2•0•Updated Apr 8, 2025Apr 8, 2025

• rrp-workshop-exercises

  Public
  Materials for reproducible research practices workshop exercises.

  HTML

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  Other

  •49•1•0•0•Updated Apr 2, 2025Apr 2, 2025

• 2025-march-training

  Public
  HTML

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  Other

  •0•0•0•0•Updated Mar 19, 2025Mar 19, 2025

• resources-portal

  Public
  Python

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

  •1•1•88•4•Updated Mar 6, 2025Mar 6, 2025

• refinebio-examples

  Public
  Example workflows for refine.bio data

  gene-expressionpathway-analysisdifferential-expression+ 2notebookbiodata

  HTML

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  Other

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

• 2024-december-training

  Public
  HTML

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  Other

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

• refinebio-js

  Public
  Javascript client for refine.bio

  JavaScript

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  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

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  Other

  •3•1•16•0•Updated Oct 18, 2024Oct 18, 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

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  Other

  •20•132•489•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

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  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

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

  •9•0•0•0•Updated Jul 16, 2024Jul 16, 2024

• spellcheck

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

  R

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  MIT License

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