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    81 repositories

    • OpenScPCA-nf

      Public
      A workflow for running OpenScPCA analysis modules
      R
      •
      BSD 3-Clause "New" or "Revised" License
      •0•1•11•0•Updated May 1, 2026May 1, 2026

    • 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
      bioinformaticssingle-cell
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•4•58•2•Updated May 1, 2026May 1, 2026

    • 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•134•492•12•Updated May 1, 2026May 1, 2026

    • 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
      •33•72•42•1•Updated May 1, 2026May 1, 2026

    • medulloblastoma-classifier

      Public
      HTML
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•18•0•Updated Apr 28, 2026Apr 28, 2026

    • scpca-nf

      Public
      scpca-nf is the Nextflow workflow for processing Single-cell Pediatric Cancer Atlas Portal data
      nextflowscrna-seq10xgenomics
      nextflowscrna-seq10xgenomicsspatial-transcriptomicscite-seqrna-seq-quantificationalevin-fry
      R
      •
      BSD 3-Clause "New" or "Revised" License
      •2•13•53•2•Updated Apr 27, 2026Apr 27, 2026

    • 2026-may-training

      Public
      HTML
      •
      Other
      •0•0•2•0•Updated Apr 27, 2026Apr 27, 2026

    • 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 Apr 21, 2026Apr 21, 2026

    • scpca-docs

      Public
      User information about ScPCA processing
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•14•0•Updated Apr 17, 2026Apr 17, 2026

    • scpcaTools

      Public
      R
      •
      BSD 3-Clause "New" or "Revised" License
      •0•1•12•0•Updated Apr 9, 2026Apr 9, 2026

    • rOpenScPCA

      Public
      R package to support analysis in the OpenScPCA project
      HTML
      •
      Other
      •2•0•7•2•Updated Apr 6, 2026Apr 6, 2026

    • scrumlord

      Public
      Continuous administration of the Greene Lab's electronic scrum
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •10•0•0•0•Updated Mar 13, 2026Mar 13, 2026

    • ScPCA-manuscript

      Public
      The manuscript repository for the Single-cell Pediatric Cancer Atlas (ScPCA)
      HTML
      •
      Creative Commons Attribution 4.0 International
      •1•0•18•0•Updated Feb 10, 2026Feb 10, 2026

    • scpca-paper-figures

      Public
      Figures for https://github.com/AlexsLemonade/ScPCA-manuscript/
      HTML
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•2•0•Updated Feb 10, 2026Feb 10, 2026

    • OpenScPCA-analysis

      Public
      An open, collaborative project to analyze data from the Single-cell Pediatric Cancer Atlas (ScPCA) Portal
      opensciencesingle-cell
      opensciencesingle-cell
      HTML
      •
      Other
      •23•15•43•2•Updated Feb 5, 2026Feb 5, 2026

    • .github

      Public
      1•0•0•0•Updated Jan 7, 2026Jan 7, 2026

    • ScPCAr

      Public
      An R package for interacting with the ScPCA Portal API
      R
      •
      Other
      •0•0•3•0•Updated Dec 17, 2025Dec 17, 2025

    • 2025-december-training

      Public
      HTML
      •
      Other
      •0•0•0•0•Updated Dec 9, 2025Dec 9, 2025

    • mbSSP

      Public
      Single Sample Predictor for Medulloblastoma Samples
      R
      •
      Other
      •0•0•1•0•Updated Dec 2, 2025Dec 2, 2025

    • reproducible-research

      Public
      Repository for Reproducible Research Practices Training Workshop
      HTML
      •
      Other
      •2•1•13•1•Updated Nov 7, 2025Nov 7, 2025

    • rrp-workshop-exercises

      Public
      Materials for reproducible research practices workshop exercises.
      HTML
      •
      Other
      •63•1•0•0•Updated Nov 3, 2025Nov 3, 2025

    • 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•5•0•Updated Oct 1, 2025Oct 1, 2025

    • 2025-august-training

      Public
      HTML
      •
      Other
      •0•0•0•0•Updated Aug 8, 2025Aug 8, 2025

    • 2025-june-training

      Public
      HTML
      •
      Other
      •0•0•0•0•Updated Jun 9, 2025Jun 9, 2025

    • refinebio-web

      Public
      Refinebio Web
      JavaScript
      •
      BSD 3-Clause "New" or "Revised" License
      •0•1•34•0•Updated May 29, 2025May 29, 2025

    • 2025-treehouse-training

      Public
      Reproducible Research Practices and Code Review Workshop for UCSC Treehouse Childhood Cancer Initiative
      Shell
      •
      Creative Commons Attribution 4.0 International
      •0•0•2•0•Updated Apr 8, 2025Apr 8, 2025

    • 2025-march-training

      Public
      HTML
      •
      Other
      •0•0•0•0•Updated Mar 19, 2025Mar 19, 2025

    • resources-portal

      Public
      Python
      •
      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
      notebookgene-expressionpathway-analysis
      notebookgene-expressionpathway-analysisdifferential-expressionbiodata
      HTML
      •
      Other
      •7•11•32•1•Updated Jan 14, 2025Jan 14, 2025

    • 2024-december-training

      Public
      HTML
      •
      Other
      •0•0•0•0•Updated Dec 11, 2024Dec 11, 2024
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