Seurat
5.5.1Tools for Single Cell Genomics
79packages depend
843Kdownloads / year
–test coverage
13/13checks pass
Overview
About
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
Health
CRAN checks
13OK
Code health
Yes
Tests · ratio 0.33
not tracked
Coverage
99%
Documentation · exports
None
Vignettes
Yes
README
53
Dependencies · direct
Check history
- OK2026-06-1713 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
- NOTE2026-06-1111 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
- OK2026-06-0913 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
- ERROR2026-06-0812 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
- OK2026-04-2512 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
Show 6 earlier snapshots
- ERROR2026-04-2310 OK · 3 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
- NOTE2026-04-2211 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
- ERROR2026-04-1810 OK · 3 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
- NOTE2026-04-1011 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
- ERROR2026-04-0910 OK · 3 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
- NOTE2026-03-1011 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
Downloads
843K
CRAN downloads in the past year
Rank #410 · ~2.3K/day · ~70.2K/mo
Seurat
Daily download trend is not available in this view yet.
64.9K30 days
232.7K90 days
843K1 year
Also on9.6K r2u18 autocran124.3K conda_forge44.7K bioconda80 c2d4u
Dependencies
Declared dependencies
82 external dependencies (excludes base and recommended)
Depends (3)
R >= 4.0.0methods baseSeuratObject
Imports (51)
cluster basecowplotfastDummiesfitdistrplusfuturefuture.applygenericsggplot2ggrepelggridgesgraphics basegrDevices basegrid basehttricaigraphirlbajsonliteKernSmooth baselifecyclelmtestMASS baseMatrix (>=
1.5-0)matrixStatsminiUIpatchworkpbapplyplotly (>=
4.9.0)pngprogressrRANNRColorBrewerRcppRcppAnnoyRcppHNSWreticulaterlangROCRRSpectraRtsnescalesscattermoresctransform (>=
0.4.1)shinyspatstat.explorespatstat.geomstats basetibbletools baseutils baseuwot
LinkingTo (3)
Suggests (36)
Enhances (0)
none
Reverse dependencies
79direct
–indirect (not tracked)
scCustomizeAPackOfTheClonesAnanseSeuratCAESAR.SuiteCellDEEPCellWindXClustAssessDR.SCDWLSFIRMGeneNMFHetSeqPRECASTPopCommProFASTRepeatedHighDimSPACOSPECKSTREAKSeuratExplorerSignacXSingleCellComplexHeatMapSlideCNASlimRSoupXSpaCCIXYomicsbbknnRcoFASTmixhvgnebularPanglaoDBscDiffComscGOclustscGatescMappRscMetaTrajscPairsscRNAstatscaperscccascperturbRscpoissontidyseuratCIARACRMetricsCanekCytoSimplex
and 31 more packages.
Code
78,151Lines of code
291Exported functions
Code & tests
Open call graph →Line coverage
–
Expression
–
Tests / Examples
–
Functions
770 230 exported
Complexity
5.3 avg / 67 max
Call network
770 nodes / 793 edges
Test coverage has not been measured for this package yet; nodes fall back to a neutral fill.
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Lowest coverage
Per-function coverage is not measured for this package yet.
People & History
People (26)
Maintainer (1)
Author, Maintainer
Contributors (24)
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Funders (1)
Release timeline
48 releases. Pick two to compare their code metrics; R releases are shown for context.
- 5.5.1Latest2026-06-26 · current release
- RR 4.6.0 released · 2026-04-24
- 5.5.02026-04-22 · diff ↗
- 5.4.02025-12-14 · diff ↗
- 5.3.12025-10-29 · diff ↗
- 5.3.02025-04-24 · diff ↗
- RR 4.5.0 released · 2025-04-11
- 5.2.12025-01-24 · diff ↗
- 5.2.02025-01-14 · diff ↗
- 5.1.02024-05-10 · diff ↗
- RR 4.4.0 released · 2024-04-24
- 5.0.32024-03-19 · diff ↗
- 5.0.22024-02-29 · diff ↗
- 5.0.12023-11-18 · diff ↗
- 5.0.02023-11-04 · diff ↗
- 4.4.02023-09-28 · diff ↗
Show 41 earlier events
- 4.3.0.12023-06-22 · diff ↗
- RR 4.3.0 released · 2023-04-21
- 4.3.02022-11-19 · diff ↗
- 4.2.12022-11-08 · diff ↗
- 4.2.02022-09-22 · diff ↗
- 4.1.12022-05-02 · diff ↗
- RR 4.2.0 released · 2022-04-22
- 4.1.02022-01-14 · diff ↗
- 4.0.62021-12-16 · diff ↗
- 4.0.52021-10-17 · diff ↗
- 4.0.42021-08-20 · diff ↗
- 4.0.32021-06-10 · diff ↗
- 4.0.22021-05-21 · diff ↗
- RR 4.1.0 released · 2021-05-18
- 4.0.12021-03-18 · diff ↗
- 4.0.02021-01-30 · diff ↗
- 3.2.32020-12-15 · diff ↗
- 3.2.22020-09-26 · diff ↗
- 3.2.12020-09-07 · diff ↗
- 3.2.02020-07-16 · diff ↗
- RR 4.0.0 released · 2020-04-24
- 3.1.52020-04-16 · diff ↗
- 3.1.42020-02-26 · diff ↗
- 3.1.32020-02-11 · diff ↗
- 3.1.22019-12-12 · diff ↗
- 3.1.12019-10-03 · diff ↗
- 3.1.02019-08-20 · diff ↗
- 3.0.22019-06-15 · diff ↗
- 3.0.12019-05-16 · diff ↗
- RR 3.6.0 released · 2019-04-26
- 3.0.02019-04-15 · diff ↗
- 2.3.42018-07-20 · diff ↗
- 2.3.32018-07-03 · diff ↗
- 2.3.22018-06-12 · diff ↗
- 2.3.12018-05-05 · diff ↗
- RR 3.5.0 released · 2018-04-23
- 2.3.02018-03-23 · diff ↗
- 2.2.12018-02-14 · diff ↗
- 2.2.02018-01-10 · diff ↗
- 2.1.02017-10-12 · diff ↗
- 2.0.12017-08-22
0 of 2 selectedCompare selected
Package metadata
- First published
- 2017-08-22
- Total releases
- 48 / 9 yrs
- License
- MIT + file LICENSE OSI
- Download size
- not tracked yet
- Installed size
- not tracked yet
- With dependencies
- not tracked yet