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    87 repositories

    • snp2cell

      Public
      cell type specific, trait-associated gene regulation
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•31•0•0•Updated Sep 8, 2026Sep 8, 2026

    • ArcheTypist

      Public
      Classify scRNA-seq samples into archetypes based on cell composition
      Python
      •
      MIT License
      •0•0•0•0•Updated Sep 8, 2026Sep 8, 2026

    • cell2home

      Public
      Analyse cell homing and migration in single-cell datasets
      Python
      •
      MIT License
      •1•0•0•0•Updated Sep 8, 2026Sep 8, 2026

    • thymus-ageing

      Public
      Jupyter Notebook
      •0•1•0•0•Updated Aug 26, 2026Aug 26, 2026

    • csd3-scripts

      Public
      Various utility scripts for CSD3 survival
      Shell
      •0•1•0•0•Updated Jul 31, 2026Jul 31, 2026

    • Developing_heart_atlas

      Public
      Jupyter Notebook
      •1•4•0•0•Updated Jul 29, 2026Jul 29, 2026

    • TissueTypist

      Public
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Jul 29, 2026Jul 29, 2026

    • 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•92•10•2•Updated Jul 28, 2026Jul 28, 2026

    • thy_transp

      Public
      Repository holding all scripts to reproduce analyses for the manuscript "Transplantation of human thymus regenerates chimeric niches supporting T-cell developme…
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Jul 20, 2026Jul 20, 2026

    • HOCA

      Public
      Python
      •
      Other
      •0•1•0•0•Updated Jul 17, 2026Jul 17, 2026

    • hormone2cell

      Public
      Predict hormone producing/receiving strength in single cell datasets.
      Python
      •
      MIT License
      •1•3•0•0•Updated Jul 2, 2026Jul 2, 2026

    • cell2clone

      Public
      Infer adaptive lymphocyte clonality from single-cell transcriptomics without antigen receptor sequencing data
      Python
      •
      MIT License
      •0•0•0•0•Updated Jun 29, 2026Jun 29, 2026

    • crohns-fibroblast-atlas

      Public
      Jupyter Notebook
      •
      MIT License
      •2•2•0•0•Updated Jun 28, 2026Jun 28, 2026

    • ega-meta-harvest

      Public
      Gather EGAF-EGAN-EGAX metadata for EGA data released from Sanger
      Python
      •0•0•0•0•Updated Jun 20, 2026Jun 20, 2026

    • cell2specificity

      Public
      Python
      •
      Other
      •1•1•0•0•Updated Jun 16, 2026Jun 16, 2026

    • hypersampling

      Public
      Repository of code used in the analysis of the adult human heart hypersampling project
      Jupyter Notebook
      •0•1•0•0•Updated Jun 15, 2026Jun 15, 2026

    • ORACLE

      Public
      Oral Reference Atlas for Cell Learning and Embedding (ORACLE)
      Python
      •
      Apache License 2.0
      •0•1•0•0•Updated Jun 13, 2026Jun 13, 2026

    • celltypist

      Public
      A tool for semi-automatic cell type classification
      pythonmachine-learningscrna-seq
      pythonmachine-learningscrna-seqsingle-cellcell-type-classificationlabel-transfer
      Python
      •
      MIT License
      •59•503•46•2•Updated May 22, 2026May 22, 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 May 12, 2026May 12, 2026

    • bin2cell

      Public
      Join subcellular Visium HD bins into cells
      Python
      •
      MIT License
      •13•143•10•0•Updated May 8, 2026May 8, 2026

    • PanGIAtlas

      Public
      Integration of gut cell atlases
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •10•41•1•0•Updated May 6, 2026May 6, 2026

    • scg_lib_structs

      Public
      Collections of library structure and sequence of popular single cell genomic methods
      HTML
      •111•509•2•0•Updated Apr 16, 2026Apr 16, 2026

    • celcomen

      Public
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •3•30•3•0•Updated Apr 15, 2026Apr 15, 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
      •17•121•6•0•Updated Mar 9, 2026Mar 9, 2026

    • gene2probe

      Public
      Pipeline for designing custom probes against human genes
      Jupyter Notebook
      •
      MIT License
      •8•24•0•1•Updated Jan 30, 2026Jan 30, 2026

    • sctk

      Public
      Python
      •
      GNU General Public License v3.0
      •8•49•1•1•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

    • TissueTag

      Public
      Python package to interactively annotate histological images within a jupyter notebook
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •2•19•1•0•Updated Oct 20, 2025Oct 20, 2025
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