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    80 repositories

    • celltypist

      Public
      A tool for semi-automatic cell type classification
      pythonmachine-learningscrna-seq
      pythonmachine-learningscrna-seqsingle-cellcell-type-classificationlabel-transfer
      Python
      •
      MIT License
      •60•473•46•3•Updated May 5, 2026May 5, 2026

    • Developing_heart_atlas

      Public
      Jupyter Notebook
      •1•4•0•0•Updated May 1, 2026May 1, 2026

    • TissueTypist

      Public
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Apr 28, 2026Apr 28, 2026

    • tcellatlas_analysis_code

      Public
      Analysis and code of the manuscript 'A pan-infection single-cell atlas of human T cells unlocks systematic antigen-specificity inference'.
      Jupyter Notebook
      •0•1•0•0•Updated Apr 28, 2026Apr 28, 2026

    • scg_lib_structs

      Public
      Collections of library structure and sequence of popular single cell genomic methods
      HTML
      •109•498•2•0•Updated Apr 16, 2026Apr 16, 2026

    • celcomen

      Public
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •3•28•2•0•Updated Apr 15, 2026Apr 15, 2026

    • csd3-scripts

      Public
      Various utility scripts for CSD3 survival
      Shell
      •0•1•0•0•Updated Apr 13, 2026Apr 13, 2026

    • cell2specificity

      Public
      Python
      •
      Other
      •1•0•0•0•Updated Mar 26, 2026Mar 26, 2026

    • celltypist_wiki

      Public
      Materials and scripts for building cell type encyclopedia table
      Python
      •3•20•0•0•Updated Mar 16, 2026Mar 16, 2026

    • nichefinder

      Public
      Quantify spatial proximity patterns of cell types
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •0•1•0•0•Updated Mar 9, 2026Mar 9, 2026

    • cellhint

      Public
      A tool for semi-automatic cell type harmonization and integration
      pythonmachine-learningscrna-seq
      pythonmachine-learningscrna-seqdata-integrationsingle-cellcell-type-harmonization
      Python
      •
      MIT License
      •16•120•6•0•Updated Mar 9, 2026Mar 9, 2026

    • cell2home

      Public
      Analyse cell homing and migration in single-cell datasets
      Python
      •
      MIT License
      •1•0•0•0•Updated Mar 9, 2026Mar 9, 2026

    • crohns-fibroblast-atlas

      Public
      Jupyter Notebook
      •
      MIT License
      •1•1•0•0•Updated Feb 20, 2026Feb 20, 2026

    • gene2probe

      Public
      Pipeline for designing custom probes against human genes
      Jupyter Notebook
      •
      MIT License
      •7•22•0•1•Updated Jan 30, 2026Jan 30, 2026

    • sctk

      Public
      Python
      •
      GNU General Public License v3.0
      •8•47•1•1•Updated Jan 28, 2026Jan 28, 2026

    • ega-meta-harvest

      Public
      Gather EGAF-EGAN-EGAX metadata for EGA data released from Sanger
      Python
      •0•0•0•0•Updated Jan 28, 2026Jan 28, 2026

    • hash_custom_10x_probes

      Public
      Make unique hashes across custom 10X probe panels
      Python
      •0•1•0•0•Updated Jan 26, 2026Jan 26, 2026

    • thymus-ageing

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

    • bin2cell

      Public
      Join subcellular Visium HD bins into cells
      Python
      •
      MIT License
      •14•141•10•0•Updated Nov 4, 2025Nov 4, 2025

    • PanGIAtlas

      Public
      Integration of gut cell atlases
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •10•35•4•0•Updated Oct 29, 2025Oct 29, 2025

    • TissueTag

      Public
      Python package to interactively annotate histological images within a jupyter notebook
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •2•18•1•0•Updated Oct 20, 2025Oct 20, 2025

    • visium_stitcher

      Public
      Stitch multiple Visium slides together
      Jupyter Notebook
      •
      MIT License
      •1•16•1•0•Updated Oct 16, 2025Oct 16, 2025

    • bracer

      Public
      BraCeR - reconstruction of B cell receptor sequences from single-cell RNAseq data
      Python
      •
      Other
      •23•42•17•2•Updated Oct 15, 2025Oct 15, 2025

    • TissueTypist_ver2025

      Public
      Jupyter Notebook
      •
      MIT License
      •1•0•0•0•Updated Sep 3, 2025Sep 3, 2025

    • Genes2Genes

      Public
      Aligning gene expression trajectories of single-cell reference and query systems
      pythonscrna-seqdynamic-programming
      pythonscrna-seqdynamic-programmingbayesian-inferencesingle-cellhuman-cell-atlaspseudotime-trajectorytrajectory-alignmentminimum-message-length
      Jupyter Notebook
      •
      MIT License
      •13•88•10•2•Updated Aug 10, 2025Aug 10, 2025

    • cellregulondb

      Public
      CellRegulon database code
      Python
      •
      MIT License
      •0•3•1•0•Updated Jul 25, 2025Jul 25, 2025

    • skeletal_dev_atlas

      Public
      Jupyter Notebook
      •
      BSD 2-Clause "Simplified" License
      •2•7•2•0•Updated Jul 11, 2025Jul 11, 2025

    • cell2tcr

      Public
      Inference of TCR motifs
      Jupyter Notebook
      •
      Other
      •3•32•2•0•Updated Jun 17, 2025Jun 17, 2025

    • ThyAge-Clock

      Public
      MIT License
      •0•0•0•0•Updated Apr 16, 2025Apr 16, 2025

    • snp2cell

      Public
      cell type specific, trait-associated gene regulation
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•30•0•0•Updated Mar 31, 2025Mar 31, 2025
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