Data Structures for Single Cell Data

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) , Macosko E, Basu A, Satija R, et al (2015) , and Stuart T, Butler A, et al (2019) , Hao Y, Hao S, et al (2021) and Hao Y, et al (2023) for more details.


Reference manual

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install.packages("SeuratObject")

5.4.0 by Rahul Satija, 6 months ago


https://satijalab.github.io/seurat-object/, https://github.com/satijalab/seurat-object


Report a bug at https://github.com/satijalab/seurat-object/issues


Browse source code at https://github.com/cran/SeuratObject


Authors: Paul Hoffman [aut] , Rahul Satija [aut, cre] (ORCID: , David Collins [aut] , Yuhan Hao [aut] , Austin Hartman [aut] , Gesmira Molla [aut] , Andrew Butler [aut] , Tim Stuart [aut] , Madeline Kowalski [ctb] (ORCID: , Saket Choudhary [ctb] , Skylar Li [ctb] , Longda Jiang [ctb] , Anagha Shenoy [ctb] , Jeff Farrell [ctb] , Shiwei Zheng [ctb] , Christoph Hafemeister [ctb] (ORCID: , Patrick Roelli [ctb]


Documentation:   PDF Manual  


MIT + file LICENSE license


Imports future, future.apply, generics, grDevices, grid, lifecycle, Matrix, methods, progressr, Rcpp, rlang, spam, stats, tools, utils

Depends on sp

Suggests BPCells, DelayedArray, fs, sf, ggplot2, HDF5Array, rmarkdown, testthat

Linking to Rcpp, RcppEigen


Imported by APackOfTheClones, RepeatedHighDim, SCIntRuler, SeuratExplorer, Signac, XYomics, bbknnR, influential, scCustomize, scFlex, scPairs, scaper, scpoisson.

Depended on by Seurat, tidyseurat.

Suggested by CellWindX, ClustAssess, CytoSimplex, IOBR, RESET, RGraphSpace, SCpubr, SPECK, SigBridgeRUtils, SingleCellComplexHeatMap, SpaTopic, VAM, biocohort, celliverse, citcdf, gedi2, ggmlR, lstar, mascarade, mxfda, myTAI, rliger, scOntoMatch, singleCellHaystack, spatialGE.


See at CRAN