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    71 repositories

    • OpenScPCA-analysis

      Public
      An open, collaborative project to analyze data from the Single-cell Pediatric Cancer Atlas (ScPCA) Portal
      opensciencesingle-cell
      HTML
      •
      Other
      •14•5•26•4•Updated Oct 8, 2024Oct 8, 2024

    • OpenScPCA-nf

      Public
      A workflow for running OpenScPCA analysis modules
      R
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•4•1•Updated Oct 7, 2024Oct 7, 2024

    • scpca-nf

      Public
      scpca-nf is the Nextflow workflow for processing Single-cell Pediatric Cancer Atlas Portal data
      nextflowscrna-seq10xgenomicsspatial-transcriptomicscite-seqrna-seq-quantificationalevin-fry
      R
      •
      BSD 3-Clause "New" or "Revised" License
      •2•12•22•1•Updated Oct 7, 2024Oct 7, 2024

    • refinebio-web

      Public
      Refinebio Web
      JavaScript
      •
      BSD 3-Clause "New" or "Revised" License
      •0•1•42•7•Updated Oct 7, 2024Oct 7, 2024

    • 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•41•2•Updated Oct 7, 2024Oct 7, 2024

    • medulloblastoma-classifier

      Public
      HTML
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•13•1•Updated Oct 3, 2024Oct 3, 2024

    • scpca-docs

      Public
      User information about ScPCA processing
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•14•0•Updated Oct 1, 2024Oct 1, 2024

    • reproducible-research

      Public
      Repository for Reproducible Research Practices Training Workshop
      HTML
      •
      Other
      •3•1•14•0•Updated Sep 19, 2024Sep 19, 2024

    • rrp-workshop-exercises

      Public
      Materials for reproducible research practices workshop exercises.
      HTML
      •
      Other
      •39•1•0•0•Updated Sep 19, 2024Sep 19, 2024

    • scpcaTools

      Public
      R
      •
      BSD 3-Clause "New" or "Revised" License
      •0•1•8•0•Updated Sep 5, 2024Sep 5, 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
      •19•129•471•14•Updated Sep 3, 2024Sep 3, 2024

    • refinebio-js

      Public
      Javascript client for refine.bio
      JavaScript
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•7•7•Updated Aug 31, 2024Aug 31, 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•10•2•Updated Aug 21, 2024Aug 21, 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
      •27•61•43•0•Updated Aug 12, 2024Aug 12, 2024

    • training-specific-template

      Public template
      Template repository that can be cloned to create repo for administering a specific training workshop
      HTML
      •
      Other
      •2•0•3•0•Updated Aug 8, 2024Aug 8, 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

    • 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 Apr 18, 2024Apr 18, 2024

    • scpca-paper-figures

      Public
      Figures for https://github.com/AlexsLemonade/ScPCA-manuscript/
      R
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•3•0•Updated Apr 17, 2024Apr 17, 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

    • resources-portal

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•1•88•5•Updated Feb 5, 2024Feb 5, 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

    • ccdatalab-gifs

      Public
      Hosting gifs for ccdatalab.org
      0•0•0•0•Updated Dec 15, 2023Dec 15, 2023

    • refinebio-docs

      Public
      User Documentation for refine.bio
      Creative Commons Attribution 4.0 International
      •4•1•15•0•Updated Sep 12, 2023Sep 12, 2023

    • sc-data-integration

      Public
      HTML
      •0•0•12•0•Updated Sep 1, 2023Sep 1, 2023

    • scpca-downstream-analyses

      Public
      This repository is intended to store our pipeline for marker genes analysis.
      R
      •0•0•4•0•Updated Aug 16, 2023Aug 16, 2023