Repositories list

• thymusatlasanalysis

  Public
  Analysis for our 2018 Immunity paper (cell atlas of mouse thymus development).

  R

  •1•3•1•0•Updated Aug 13, 2025Aug 13, 2025

• epigenetic_characterization_hPFEv1

  Public
  Jupyter Notebook

  •0•0•0•0•Updated Aug 17, 2023Aug 17, 2023

• cellmatch

  Public
  R

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Aug 1, 2023Aug 1, 2023

• de_screen_analysis

  Public
  Code to reproduce our analyses from the definitive endoderm screen, April 2019 Cell Reports

  Python

  •1•1•0•0•Updated Feb 7, 2022Feb 7, 2022

• pharyngeal_endoderm_development

  Public
  Jupyter Notebook

  •2•9•0•0•Updated Jan 27, 2022Jan 27, 2022

• thymusatlastools2

  Public
  A set of general purpose tools for single cell analysis. Upgrade of thymusatlastools, also available on our Github.

  R

  •0•3•0•0•Updated Jan 6, 2022Jan 6, 2022

• de_screen_atacTFAP

  Public
  Implementation of the atacTFAP analysis in our DE screen paper (April 2018 Cell Reports)

  R

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

• bubblegrid

  Public
  Bubble grid plots for single-cell omics data

  R

  •

  Other

  •0•0•0•0•Updated Feb 7, 2019Feb 7, 2019

• ggbio

  Public
  Grid and ggplot2 based visualization for biological data

  R

  •26•1•0•0•Updated Oct 12, 2018Oct 12, 2018

• seurat

  Public
  R toolkit for single cell genomics

  R

  •

  GNU General Public License v3.0

  •972•1•0•0•Updated Sep 27, 2018Sep 27, 2018

• thymusatlastools

  Public
  R package to accompany our recent Immunity paper on the mouse thymus developmental cell atlas.

  R

  •1•5•0•0•Updated May 29, 2018May 29, 2018