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    32 repositories

    • homebrew-r-srf

      Public
      Custom Homebrew R formula with tcl-tk support and additional options
      Ruby
      •16•0•0•0•Updated Oct 28, 2024Oct 28, 2024

    • cole-trapnell-lab.github.io

      Public
      HTML
      •12•13•3•4•Updated Sep 26, 2024Sep 26, 2024

    • hooke

      Public
      A package for comparing cell type abundances between conditions
      R
      •
      Other
      •1•5•18•0•Updated Sep 25, 2024Sep 25, 2024

    • monocle3

      Public
      single-cell-rna-seq
      R
      •
      Other
      •100•333•236•3•Updated Sep 6, 2024Sep 6, 2024

    • cicero-release

      Public
      R
      •
      MIT License
      •15•56•10•0•Updated Sep 3, 2024Sep 3, 2024

    • leidenbase

      Public
      C
      •13•13•13•2•Updated Jul 22, 2024Jul 22, 2024

    • cicero

      Public
      R
      •
      MIT License
      •9•11•0•0•Updated Feb 6, 2024Feb 6, 2024

    • sci-Plex-GxE

      Public
      Repository of analysis code for sci-Plex-GxE analysis
      R
      •
      MIT License
      •1•2•0•0•Updated Dec 7, 2023Dec 7, 2023

    • sdg-zfish

      Public
      R
      •1•1•0•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

    • garnett

      Public
      Automated cell type classification
      R
      •
      MIT License
      •25•105•6•0•Updated Aug 4, 2023Aug 4, 2023

    • monocle-release

      Public
      R
      •116•279•310•8•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
      •16•27•5•0•Updated Jul 1, 2020Jul 1, 2020

    • sci-plex

      Public
      repository containing analysis scripts and auxiliary files
      R
      •2•30•3•0•Updated Apr 9, 2020Apr 9, 2020

    • cufflinks

      Public
      C++
      •
      Boost Software License 1.0
      •116•310•84•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•8•1•0•Updated Mar 25, 2020Mar 25, 2020

    • Scribe

      Public
      Regulatory networks with Direct Information
      C++
      •6•16•7•0•Updated Oct 14, 2019Oct 14, 2019

    • pseudospace

      Public
      R
      •4•11•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++
      •4•4•2•0•Updated May 22, 2018May 22, 2018

    • worm-rna

      Public
      The C. elegans transcriptome at single cell resolution
      Jupyter Notebook
      •7•11•4•0•Updated Mar 28, 2018Mar 28, 2018

    • scRNASeqSim

      Public
      A simulator for measuring developmental trajectories with single-cell RNA-seq
      R
      •0•5•0•0•Updated Oct 4, 2017Oct 4, 2017

    • rccm

      Public
      A modified cross-convergence mapping library
      R
      •
      Other
      •0•1•0•0•Updated Oct 4, 2017Oct 4, 2017

    • monocle

      Public
      This is a read-only mirror of the Bioconductor SVN repository. Package Homepage: http://bioconductor.org/packages/devel/bioc/html/monocle.html Bug Reports: https://support.bioconductor.org/p/new/post/?tag_val=monocle.
      R
      •0•2•0•0•Updated May 16, 2016May 16, 2016

    • tuxsim

      Public
      C++
      •
      Other
      •1•0•0•1•Updated Oct 28, 2015Oct 28, 2015