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    36 repositories

    • platt

      Public
      R
      •
      MIT License
      •0•4•12•0•Updated Jul 14, 2026Jul 14, 2026

    • cole-trapnell-lab.github.io

      Public
      HTML
      •12•14•3•4•Updated Jun 2, 2026Jun 2, 2026

    • monocle3

      Public
      single-cell-rna-seq
      single-cell-rna-seq
      R
      •
      Other
      •116•459•251•8•Updated May 26, 2026May 26, 2026

    • hooke

      Public
      A package for comparing cell type abundances between conditions
      R
      •
      Other
      •1•11•20•0•Updated May 20, 2026May 20, 2026

    • leidenbase

      Public
      C
      •13•15•13•2•Updated May 20, 2026May 20, 2026

    • trapnell-cluster

      Public
      Common scripts for working on the cluster
      Shell
      •2•0•0•0•Updated Apr 1, 2026Apr 1, 2026

    • cicero-release

      Public
      R
      •
      MIT License
      •16•59•11•1•Updated Mar 18, 2026Mar 18, 2026

    • cicero

      Public
      R
      •
      MIT License
      •9•12•0•0•Updated Mar 18, 2026Mar 18, 2026

    • homebrew-trapnell

      Public
      Custom Homebrew R formula with accelerated linear algebra support
      Ruby
      •1•3•0•0•Updated Oct 8, 2025Oct 8, 2025

    • garnett

      Public
      Automated cell type classification
      R
      •
      MIT License
      •29•116•8•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

    • 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•1•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
      •17•0•0•0•Updated Oct 17, 2023Oct 17, 2023

    • monocle-release

      Public
      R
      •128•295•318•10•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•39•3•0•Updated Apr 9, 2020Apr 9, 2020

    • cufflinks

      Public
      C++
      •
      Boost Software License 1.0
      •115•322•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
      •4•9•1•0•Updated Mar 25, 2020Mar 25, 2020

    • Scribe

      Public
      Regulatory networks with Direct Information
      C++
      •6•19•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•7•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
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