Repositories list

• csd3-scripts

  Public
  Various utility scripts for CSD3 survival

  Python

  •0•0•0•0•Updated Oct 20, 2025Oct 20, 2025

• TissueTag

  Public
  Python package to interactively annotate histological images within a jupyter notebook

  Jupyter Notebook

  •

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

  •2•17•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

• celltypist

  Public
  A tool for semi-automatic cell type classification

  pythonmachine-learningscrna-seq+ 3single-cellcell-type-classificationlabel-transfer

  Python

  •

  MIT License

  •49•414•40•1•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

• celltypist_wiki

  Public
  Materials and scripts for building cell type encyclopedia table

  Python

  •3•20•0•0•Updated Oct 15, 2025Oct 15, 2025

• ega-meta-harvest

  Public
  Gather EGAF-EGAN-EGAX metadata for EGA data released from Sanger

  Python

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

• TissueTypist

  Public
  Jupyter Notebook

  •

  MIT License

  •0•0•0•0•Updated Sep 3, 2025Sep 3, 2025

• Developing_heart_atlas

  Public
  Jupyter Notebook

  •0•3•0•0•Updated Aug 29, 2025Aug 29, 2025

• celcomen

  Public
  Jupyter Notebook

  •0•16•0•0•Updated Aug 20, 2025Aug 20, 2025

• sctk

  Public
  Python

  •

  GNU General Public License v3.0

  •8•41•2•1•Updated Aug 13, 2025Aug 13, 2025

• Genes2Genes

  Public
  Aligning gene expression trajectories of single-cell reference and query systems

  pythonscrna-seqdynamic-programming+ 6bayesian-inferencesingle-cellhuman-cell-atlaspseudotime-trajectorytrajectory-alignmentminimum-message-length

  Jupyter Notebook

  •

  MIT License

  •9•76•8•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•6•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

• crohns-fibroblast-atlas

  Public
  Jupyter Notebook

  •

  MIT License

  •1•1•0•0•Updated Jun 15, 2025Jun 15, 2025

• scg_lib_structs

  Public
  Collections of library structure and sequence of popular single cell genomic methods

  HTML

  •101•482•2•0•Updated May 19, 2025May 19, 2025

• bin2cell

  Public
  Join subcellular Visium HD bins into cells

  Jupyter Notebook

  •

  MIT License

  •12•126•10•0•Updated May 16, 2025May 16, 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•29•0•0•Updated Mar 31, 2025Mar 31, 2025

• cellhint

  Public
  A tool for semi-automatic cell type harmonization and integration

  pythonmachine-learningscrna-seq+ 3data-integrationsingle-cellcell-type-harmonization

  Python

  •

  MIT License

  •15•111•6•0•Updated Mar 23, 2025Mar 23, 2025

• PanGIAtlas

  Public
  Integration of gut cell atlases

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •7•28•2•0•Updated Feb 13, 2025Feb 13, 2025

• limbcellatlas

  Public
  This repository contains codes used for the human fetal limb cell atlas.

  Jupyter Notebook

  •6•17•0•0•Updated Jan 28, 2025Jan 28, 2025

• drug2cell

  Public
  Gene group activity utility functions for Scanpy

  Jupyter Notebook

  •

  Other

  •4•93•7•0•Updated Dec 21, 2024Dec 21, 2024

• vascular_atlas

  Public
  Repo with analysis code for the vascular atlas paper

  Jupyter Notebook

  •5•9•0•0•Updated Nov 22, 2024Nov 22, 2024

• thymus_spatial_atlas

  Public
  general repo that holds all analysis and figures for the thymus spatial atlas by Yayon, Kedlian, Boehme, Radtke and many more!

  genomicshumanimmunology+ 5single-cellthymusbioinformatics-toolspatial-transcriptomicscommon-coordinate-framwork

  Jupyter Notebook

  •1•11•2•0•Updated Nov 20, 2024Nov 20, 2024

• gene2probe

  Public
  Pipeline for designing custom probes against human genes

  Jupyter Notebook

  •

  MIT License

  •5•18•0•1•Updated Nov 11, 2024Nov 11, 2024

• lung-immune-cell-atlas

  Public
  This is a folder containing information of the human fetal lung leukocyte atlas

  HTML

  •2•1•0•0•Updated Nov 7, 2024Nov 7, 2024

• G2G_notebooks

  Public
  Analysis notebooks for G2G MS

  Jupyter Notebook

  •0•7•0•0•Updated Oct 7, 2024Oct 7, 2024

• ALI_COVID19

  Public
  Repo with analysis code for the ALI_COVID19 paper

  Jupyter Notebook

  •1•5•1•0•Updated Aug 2, 2024Aug 2, 2024