Repositories list

• platt

  Public
  R

  •

  MIT License

  •0•3•12•0•Updated Jan 13, 2026Jan 13, 2026

• monocle3

  Public
  single-cell-rna-seq

  R

  •

  Other

  •114•432•256•3•Updated Jan 8, 2026Jan 8, 2026

• hooke

  Public
  A package for comparing cell type abundances between conditions

  R

  •

  Other

  •1•10•20•0•Updated Jan 8, 2026Jan 8, 2026

• cole-trapnell-lab.github.io

  Public
  HTML

  •12•14•3•4•Updated Dec 18, 2025Dec 18, 2025

• homebrew-trapnell

  Public
  Custom Homebrew R formula with accelerated linear algebra support

  Ruby

  •1•3•0•0•Updated Oct 8, 2025Oct 8, 2025

• trapnell-cluster

  Public
  Common scripts for working on the cluster

  Shell

  •1•0•0•0•Updated Sep 15, 2025Sep 15, 2025

• leidenbase

  Public
  C

  •13•13•13•2•Updated Mar 31, 2025Mar 31, 2025

• garnett

  Public
  Automated cell type classification

  R

  •

  MIT License

  •29•116•7•0•Updated Jan 3, 2025Jan 3, 2025

• homebrew-r-srf

  Public archive
  Custom Homebrew R formula with tcl-tk support and additional options

  Ruby

  •18•0•0•0•Updated Dec 9, 2024Dec 9, 2024

• cicero-release

  Public
  R

  •

  MIT License

  •16•59•11•1•Updated Sep 3, 2024Sep 3, 2024

• cicero

  Public
  R

  •

  MIT License

  •9•12•0•0•Updated Feb 6, 2024Feb 6, 2024

• speedglm

  Public
  beta version

  R

  •3•0•0•0•Updated Jan 12, 2024Jan 12, 2024

• sci-Plex-GxE

  Public
  Repository of analysis code for sci-Plex-GxE analysis

  R

  •

  MIT License

  •2•4•0•0•Updated Dec 7, 2023Dec 7, 2023

• sdg-zfish

  Public
  R

  •1•2•1•0•Updated Nov 15, 2023Nov 15, 2023

• hotfish

  Public
  HTML

  •0•0•0•0•Updated Nov 1, 2023Nov 1, 2023

• PLNmodels

  Public
  A collection of Poisson lognormal models for multivariate count data analysis

  R

  •

  GNU General Public License v3.0

  •18•0•0•0•Updated Oct 17, 2023Oct 17, 2023

• monocle-release

  Public
  R

  •124•291•318•9•Updated Jul 15, 2022Jul 15, 2022

• sdg-mutant-paper-code

  Public
  Github repository containing our analysis code

  0•0•0•0•Updated May 2, 2022May 2, 2022

• sci-Space

  Public
  Contains all the code used in the analysis of the sci-Space paper

  R

  •2•2•0•0•Updated Apr 16, 2021Apr 16, 2021

• monocle2-rge-paper

  Public
  Scripts needed to generate the figures for the Monocle 2 paper (Qiu et al, 2017)

  Jupyter Notebook

  •17•29•5•0•Updated Jul 1, 2020Jul 1, 2020

• sci-plex

  Public
  repository containing analysis scripts and auxiliary files

  R

  •3•36•3•0•Updated Apr 9, 2020Apr 9, 2020

• cufflinks

  Public
  C++

  •

  Boost Software License 1.0

  •115•320•85•4•Updated Mar 31, 2020Mar 31, 2020

• yeast_umap

  Public
  Using UMAP on gene expression data from single-gene deletion strains of yeast to identify gene interactions

  R

  •3•9•1•0•Updated Mar 25, 2020Mar 25, 2020

• Scribe

  Public
  Regulatory networks with Direct Information

  C++

  •6•17•8•0•Updated Oct 14, 2019Oct 14, 2019

• pseudospace

  Public
  R

  •5•12•1•0•Updated Sep 4, 2019Sep 4, 2019

• ATAC-Pipeline-Dev

  Public
  Python

  •0•0•9•0•Updated Feb 1, 2019Feb 1, 2019

• RANNinf

  Public
  C++

  •0•0•0•0•Updated Nov 19, 2018Nov 19, 2018

• L1-graph

  Public
  R

  •0•0•1•0•Updated Aug 27, 2018Aug 27, 2018

• DDRTree

  Public
  An R implementation of the DDRTree algorithm for learning principal graphs

  C++

  •5•6•2•0•Updated May 22, 2018May 22, 2018

• worm-rna

  Public
  The C. elegans transcriptome at single cell resolution

  Jupyter Notebook

  •6•11•4•0•Updated Mar 28, 2018Mar 28, 2018