Seurat

Overview

About

Maintained by Rahul SatijaFirst published 2017-08-2248 releasesCRAN page ↗GitHub ↗

A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. 'Seurat' aims to enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. See Satija R, Farrell J, Gennert D, et al (2015) doi:10.1038/nbt.3192, Macosko E, Basu A, Satija R, et al (2015) doi:10.1016/j.cell.2015.05.002, Stuart T, Butler A, et al (2019) doi:10.1016/j.cell.2019.05.031, and Hao, Hao, et al (2020) doi:10.1101/2020.10.12.335331 for more details.

Install

R (CRAN)pak (dev)Ubuntu (r2u)openSUSE (OBS)

install.packages("Seurat", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("satijalab/seurat")

Development version from satijalab/seurat. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-seurat

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-Seurat

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

13OK

Slowest check: 20.2 min · r-devel-linux-x86_64-fedora-clang

Code health

Yes

Tests · ratio 0.33

34.3%

Coverage · measured lines

99%

Documentation · exports

53

Dependencies · direct

Check history

OK2026-06-17
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-06-11
11 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 6 earlier snapshots

ERROR2026-04-23
10 OK · 3 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-04-22
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
10 OK · 3 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-04-10
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-09
10 OK · 3 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 166 wordsVignettesNopkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 53%
Documented parameters: 97%
Return-value docs: 86%
References docs: 5%

Downloads

854.7K

CRAN downloads in the past year

Rank #418 · ~2.3K/day · ~71.2K/mo

Releases R versions

Daily download trend is not available in this view yet.

74.3K30 days

216.6K90 days

854.7K1 year

Compare downloads with other packages →

Also on9.6K r2u6 autocran124.3K conda_forge44.7K bioconda80 c2d4u

Repository

GitHub ↗ satijalab/seurat

2,774Stars

993Forks

182Open issues

37Open PRs

48Releases

9,495Commits

146Contributors

human-cell-atlassingle-cell-rna-seqsingle-cell-genomicscran

9,495 commits · Last activity 2026-07-14 · +0.7% stars, 30d

Stars over time

2025-07-24 · 2,4462026-07-20 · 2,770

Repository practices

Upstream repositoryBeta

5 development-tooling and community-health practices detected across 5 families in the upstream repository

Checks run against github.com/satijalab/seurat on 2026-07-19.

Continuous integration (1)

GitHub Actions

CRAN release process (1)

cran-comments.md

Lint, format, editor (1)

RStudio project

Governance and community (1)

Issue templates

Show all practices

Git structural (1)

.gitattributes

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

82 external dependencies (excludes base and recommended)

Depends (3)

R >= 4.0.0methodsSeuratObject

Imports (51)

clustercowplot fastDummies fitdistrplus future future.apply generics ggplot2 ggrepel ggridgesgraphicsgrDevicesgridhttr ica igraph irlba jsonliteKernSmoothlifecycle lmtestMASSMatrix (>= 1.5-0)matrixStats miniUI patchwork pbapply plotly (>= 4.9.0)png progressr RANN RColorBrewer Rcpp RcppAnnoy RcppHNSW reticulate rlang ROCR RSpectra Rtsne scales scattermore sctransform (>= 0.4.1)shiny spatstat.explore spatstat.geomstatstibbletoolsutilsuwot

LinkingTo (3)

Rcpp RcppEigen RcppProgress

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

81direct

0indirect

and 33 more packages.

People & History

People (26)

Maintainer (1)

Rahul Satija

Author, Maintainer

Authors (1)

Rahul Satija

Author, Maintainer

Contributors (24)

Andrew Butler

Contributor

Saket Choudhary

Contributor · added in 4.0.0

David Collins

Contributor · added in 5.1.0

Charlotte Darby

Contributor · added in 4.0.0

Jeff Farrell

Contributor

Isabella Grabski

Contributor · added in 5.0.0

Christoph Hafemeister

Contributor

Yuhan Hao

Contributor · added in 3.1.0

Show 16 more contributors

Austin Hartman

Contributor · added in 4.3.0

Paul Hoffman

Contributor

Jaison Jain

Contributor · added in 4.0.0

Longda Jiang

Contributor · added in 5.0.0

Madeline Kowalski

Contributor · added in 4.3.0

Skylar Li

Contributor · added in 5.0.0

Gesmira Molla

Contributor · added in 5.0.0

Efthymia Papalexi

Contributor · added in 4.0.0

Patrick Roelli

Contributor

Karthik Shekhar

Contributor · added in 4.0.0

Anagha Shenoy

Contributor · added in 5.3.1

Avi Srivastava

Contributor · added in 4.0.0

Tim Stuart

Contributor · added in 3.0.0

Kristof Torkenczy

Contributor · added in 4.0.0

Brian Zhang

Contributor · added in 5.3.1

Shiwei Zheng

Contributor

Funders (1)

Satija Lab and Collaborators

Funder · added in 4.0.0

Package Timeline

48 releases. Pick two to compare their code metrics. R releases are shown for context.

5.5.1Latest
2026-06-26 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
5.5.0
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5.3.1
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R
R 4.5.0 released · 2025-04-11
5.2.1
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5.1.0
2024-05-10 · diff ↗
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R 4.4.0 released · 2024-04-24
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5.0.1
2023-11-18 · diff ↗
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4.4.0
2023-09-28 · diff ↗

Show 44 earlier events

4.3.0.1
2023-06-22 · diff ↗
R
R 4.3.0 released · 2023-04-21
4.3.0
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4.2.1
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2022-09-22 · diff ↗
4.1.1
2022-05-02 · diff ↗
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R 4.2.0 released · 2022-04-22
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R 4.1.0 released · 2021-05-18
4.0.1
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4.0.0
2021-01-30 · diff ↗
3.2.3
2020-12-15 · diff ↗
3.2.2
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3.2.1
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2020-07-16 · diff ↗
R
R 4.0.0 released · 2020-04-24
3.1.5
2020-04-16 · diff ↗
3.1.4
2020-02-26 · diff ↗
3.1.3
2020-02-11 · diff ↗
unarchivedReturned to CRAN
2020-02-11
archivedRemoved from CRAN
2020-02-07
check issues were not corrected in time
3.1.2
2019-12-12 · diff ↗
3.1.1
2019-10-03 · diff ↗
3.1.0
2019-08-20 · diff ↗
3.0.2
2019-06-15 · diff ↗
3.0.1
2019-05-16 · diff ↗
R
R 3.6.0 released · 2019-04-26
3.0.0
2019-04-15 · diff ↗
2.3.4
2018-07-20 · diff ↗
2.3.3
2018-07-03 · diff ↗
2.3.2
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2.3.1
2018-05-05 · diff ↗
R
R 3.5.0 released · 2018-04-23
2.3.0
2018-03-23 · diff ↗
2.2.1
2018-02-14 · diff ↗
2.2.0
2018-01-10 · diff ↗
2.1.0
2017-10-12 · diff ↗
2.0.1
2017-08-22
R
R 3.4.0 released · 2017-04-21

Package metadata

First published: 2017-08-22
Total releases: 48 / 9 yrs
License: MIT + file LICENSE OSI
Additional repositories: satijalab.r-universe.dev, bnprks.r-universe.dev
Minimum R: ≥ 4.0.0
Bundled data: 1.0 KB / 2 files
Download size: 2.0 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

Overview

Install

Health

Documentation

Downloads

Repository

Repository practices

Dependencies

Code & Tests

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Package metadata