doi:10.1038/nbt.3192>, Macosko E, Basu A, Satija R, et al (2015) <doi:10.1016/j.cell.2015.05.002>, and Stuart T, Butler A, et al (2019) <doi:10.1016/j.cell.2019.05.031>, Hao Y, Hao S, et al (2021) <doi:10.1016/j.cell.2021.04.048> and Hao Y, et al (2023) <doi:10.1101/2022.02.24.481684> for more details.">

SeuratObject: Data Structures for Single Cell Data (original) (raw)

Defines S4 classes for single-cell genomic data and associated information, such as dimensionality reduction embeddings, nearest-neighbor graphs, and spatially-resolved coordinates. Provides data access methods and R-native hooks to ensure the Seurat object is familiar to other R users. 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>, and Stuart T, Butler A, et al (2019) <doi:10.1016/j.cell.2019.05.031>, Hao Y, Hao S, et al (2021) <doi:10.1016/j.cell.2021.04.048> and Hao Y, et al (2023) <doi:10.1101/2022.02.24.481684> for more details.

Version: 5.2.0
Depends: R (≥ 4.1.0), sp (≥ 1.5.0)
Imports: future, future.apply, generics, grDevices, grid, lifecycle, Matrix (≥ 1.6.4), methods, progressr, Rcpp (≥ 1.0.5), rlang (≥ 0.4.7), spam, stats, tools, utils
LinkingTo: Rcpp, RcppEigen
Suggests: BPCells, DelayedArray, fs (≥ 1.5.2), sf (≥ 1.0.0), ggplot2, HDF5Array, rmarkdown, testthat
Published: 2025-08-27
DOI: 10.32614/CRAN.package.SeuratObject
Author: Paul Hoffman ORCID iD [aut], Rahul Satija ORCID iD [aut, cre], David Collins ORCID iD [aut], Yuhan Hao ORCID iD [aut], Austin Hartman ORCID iD [aut], Gesmira Molla ORCID iD [aut], Andrew Butler ORCID iD [aut], Tim Stuart ORCID iD [aut], Madeline Kowalski ORCID iD [ctb], Saket Choudhary ORCID iD [ctb], Skylar Li [ctb], Longda Jiang ORCID iD [ctb], Anagha Shenoy ORCID iD [ctb], Jeff Farrell [ctb], Shiwei Zheng ORCID iD [ctb], Christoph HafemeisterORCID iD [ctb], Patrick Roelli [ctb]
Maintainer: Rahul Satija
BugReports: https://github.com/satijalab/seurat-object/issues
License: MIT + file
URL: https://satijalab.github.io/seurat-object/,https://github.com/satijalab/seurat-object
NeedsCompilation: yes
Additional_repositories: https://bnprks.r-universe.dev
Materials: NEWS
In views: Omics
CRAN checks: SeuratObject results

Documentation:

Downloads:

Reverse dependencies:

Reverse depends: SCArray.sat, Seurat, tidyseurat
Reverse imports: APackOfTheClones, APL, bbknnR, CAMML, CatsCradle, CDI, ClusterFoldSimilarity, clustifyr, CSOA, CuratedAtlasQueryR, DOtools, GeomxTools, Ibex, mastR, Nebulosa, Platypus, RepeatedHighDim, scAnnotate, scaper, scCustomize, scpoisson, scRepertoire, scRNAseqApp, SeuratExplorer, Signac, SpaNorm, SpatialDecon, stPipe, XYomics
Reverse suggests: anndataR, cellpypes, ClustAssess, CoGAPS, CytoSimplex, DCATS, edgeR, escape, ggsc, HVP, MOFA2, mxfda, myTAI, projectR, RESET, rliger, sccomp, scDotPlot, scOntoMatch, SCpubr, SETA, SFEData, SimBu, SingleCellComplexHeatMap, singleCellHaystack, singleCellTK, SpatialFeatureExperiment, spatialGE, SpaTopic, SPECK, UCell, VAM

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