Repositories list

• CellOracle

  Public
  This is the alpha version of the CellOracle package

  Python

  •

  Other

  •74•434•87•3•Updated Feb 3, 2026Feb 3, 2026

• adipogenesis-reproducibility-repo

  Public
  Relevant data and code for reproducing analysis of in vivo lineage tracing adipocyte precursors in skin

  Jupyter Notebook

  •0•4•0•0•Updated Aug 7, 2025Aug 7, 2025

• newCloneCalling

  Public
  Repository detailing updated allowlisting and clonal analysis workflow

  Jupyter Notebook

  •0•9•2•0•Updated Feb 1, 2025Feb 1, 2025

• CellOracle_streamlit

  Public
  Codes for celloracle web application

  Python

  •

  Apache License 2.0

  •0•2•0•0•Updated Jan 8, 2025Jan 8, 2025

• BiddyetalWorkflow

  Public
  This repository contains our CellTag workflow, as deployed in our 2018 Biddy et al., Nature paper.

  human-cell-atlas

  human-cell-atlas

  R

  •9•32•2•0•Updated Jun 24, 2024Jun 24, 2024

• Colony-counter

  Public
  Python package for the quantificatin of number of colonies

  Jupyter Notebook

  •

  BSD 2-Clause "Simplified" License

  •12•22•1•0•Updated Apr 10, 2024Apr 10, 2024

• CellOracle.documentation

  Public
  Jupyter Notebook

  •0•3•1•0•Updated Apr 2, 2024Apr 2, 2024

• CellTag-multi-2023

  Public
  Repository for scirpts to re-produce all major analyses in the CellTag-multi paper

  Jupyter Notebook

  •0•3•0•0•Updated Oct 18, 2023Oct 18, 2023

• CellTag-Titration

  Public
  Imaging-based titration software for GFP-Celltag lentivirus

  Jupyter Notebook

  •0•0•0•0•Updated Feb 19, 2023Feb 19, 2023

• CellTagR

  Public
  This repository contains the CellTag data analysis R package to support clone calling and lineage reconstruction.

  human-cell-atlas

  human-cell-atlas

  R

  •8•21•4•0•Updated Oct 19, 2022Oct 19, 2022

• Capybara

  Public
  Capybara: A computational tool to measure cell identity and fate transitions

  R

  •10•61•6•0•Updated May 23, 2022May 23, 2022

• Capybara_reproducibility

  Public
  Reproducibility Repository for Capybara

  HTML

  •0•1•2•0•Updated Mar 29, 2022Mar 29, 2022

• CellTagViz-package

  Public
  HTML

  •

  Other

  •0•1•0•0•Updated Aug 27, 2019Aug 27, 2019

• PreviousCloneHunter

  Public
  This repository contains our CellTag CloneHunter R package for clone-calling.

  human-cell-atlas

  human-cell-atlas

  R

  •2•6•1•1•Updated Jun 10, 2019Jun 10, 2019

• CellTag-Classifier

  Public
  HTML

  •

  MIT License

  •0•6•0•0•Updated Apr 23, 2019Apr 23, 2019

• CellTagViz

  Public
  Repository of the CellTag Viz Shiny App

  human-cell-atlas

  human-cell-atlas

  HTML

  •0•1•0•0•Updated Jan 31, 2019Jan 31, 2019