Repositories list

• seurat

  Public
  R toolkit for single cell genomics

  cransingle-cell-genomicssingle-cell-rna-seq+ 1

  cransingle-cell-genomicssingle-cell-rna-seqhuman-cell-atlas

  R

  •

  Other

  •982•2.7k•248•40•Updated Mar 12, 2026Mar 12, 2026

• scSLIDE

  Public
  R

  •

  Other

  •0•8•1•2•Updated Mar 12, 2026Mar 12, 2026

• Mixscale

  Public
  R

  •2•25•17•0•Updated Mar 12, 2026Mar 12, 2026

• seurat-object

  Public
  R

  •

  Other

  •34•33•44•10•Updated Mar 3, 2026Mar 3, 2026

• AzimuthAPI

  Public

  satijalab/AzimuthAPI’s past year of commit activity
  R

  •

  MIT License

  •1•5•4•0•Updated Feb 27, 2026Feb 27, 2026

• seurat-docker

  Public

  satijalab/seurat-docker’s past year of commit activity
  Docker images of Seurat

  dockersingle-cellsingle-cell-genomics+ 2

  dockersingle-cellsingle-cell-genomicssingle-cell-analysishuman-cell-atlas

  Dockerfile

  •9•9•0•0•Updated Feb 19, 2026Feb 19, 2026

• seurat-wrappers

  Public
  Community-provided extensions to Seurat

  communitysingle-cell-genomicssingle-cell-analysis

  communitysingle-cell-genomicssingle-cell-analysis

  R

  •

  GNU General Public License v3.0

  •144•358•90•19•Updated Feb 17, 2026Feb 17, 2026

• rna-fingerprinting

  Public
  R

  •

  Other

  •1•10•0•0•Updated Feb 17, 2026Feb 17, 2026

• sctransform

  Public

  satijalab/sctransform’s past year of commit activity
  R package for modeling single cell UMI expression data using regularized negative binomial regression

  R

  •

  GNU General Public License v3.0

  •36•251•49•0•Updated Jan 10, 2026Jan 10, 2026

• panhumanpy

  Public

  satijalab/panhumanpy’s past year of commit activity
  Python

  •1•24•4•4•Updated Oct 1, 2025Oct 1, 2025

• rna-fingerprinting-data

  Public
  R

  •0•0•0•0•Updated Sep 16, 2025Sep 16, 2025

• azimuth-references

  Public
  R

  •10•26•11•1•Updated May 16, 2025May 16, 2025

• seurat-data

  Public
  Dataset distribution for Seurat

  datasetssingle-cellsingle-cell-genomics

  datasetssingle-cellsingle-cell-genomics

  R

  •

  GNU General Public License v3.0

  •45•150•38•1•Updated Mar 6, 2025Mar 6, 2025

• satijalab.r-universe.dev

  Public
  0•0•0•0•Updated Jan 7, 2025Jan 7, 2025

• azimuth_website

  Public
  HTML

  •0•1•0•1•Updated Nov 6, 2024Nov 6, 2024

• azimuth

  Public
  A Shiny web app for mapping datasets using Seurat v4

  single-cell-genomicssingle-cell-rna-seqshiny-app

  single-cell-genomicssingle-cell-rna-seqshiny-app

  HTML

  •

  GNU General Public License v3.0

  •44•145•101•6•Updated Nov 5, 2024Nov 5, 2024

• PASTA

  Public
  R

  •

  Other

  •8•21•8•1•Updated Aug 26, 2024Aug 26, 2024

• scChromHMM

  Public
  🧬 🦀 A fast and efficient tool to perform a genome wide Single cell Chromatin State Analysis using multimodal histone modification data.

  single-cellhistone-modificationschromatin-state

  single-cellhistone-modificationschromatin-state

  Rust

  •

  BSD 3-Clause "New" or "Revised" License

  •4•30•3•0•Updated Sep 9, 2021Sep 9, 2021

• azimuth-meta-analysis

  Public
  R

  •0•2•0•0•Updated Jun 14, 2021Jun 14, 2021

• AzimuthDashboard

  Public
  R

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Feb 16, 2021Feb 16, 2021

• lung-ccf

  Public
  Central repo to deposit code for lung CCF project

  Jupyter Notebook

  •0•2•0•0•Updated Feb 12, 2020Feb 12, 2020

• controls

  Public
  Jupyter Notebook

  •1•0•0•0•Updated Nov 20, 2019Nov 20, 2019

• data

  Public
  1•0•0•0•Updated Nov 20, 2019Nov 20, 2019

• Integration2019

  Public
  R

  •8•17•3•0•Updated Jun 5, 2019Jun 5, 2019

• gdown.pl

  Public
  Google Drive direct download of big files

  Perl

  •

  GNU General Public License v3.0

  •188•0•0•0•Updated Feb 3, 2019Feb 3, 2019

• hca-jamboree-how-many-cells

  Public
  MIT License

  •7•0•0•0•Updated Apr 10, 2018Apr 10, 2018