SeuratObject: 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) <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: |
5.0.2 |
| Depends: |
R (≥ 4.1.0), sp (≥ 1.5.0) |
| Imports: |
future, future.apply, grDevices, grid, Matrix (≥ 1.6.4), methods, progressr, Rcpp (≥ 1.0.5), rlang (≥ 0.4.7), stats, tools, utils, spam, lifecycle, generics |
| LinkingTo: |
Rcpp, RcppEigen |
| Suggests: |
DelayedArray, fs (≥ 1.5.2), ggplot2, HDF5Array, rmarkdown, testthat, BPCells, sf (≥ 1.0.0) |
| Enhances: |
Seurat |
| Published: |
2024-05-08 |
| DOI: |
10.32614/CRAN.package.SeuratObject |
| Author: |
Paul Hoffman 
[aut] (<https://orcid.org/0000-0002-7693-8957>),
Rahul Satija
[aut, cre] (<https://orcid.org/0000-0001-9448-8833>),
David Collins
[aut] (<https://orcid.org/0000-0001-9243-7821>),
Yuhan Hao [aut]
(<https://orcid.org/0000-0002-1810-0822>),
Austin Hartman
[aut] (<https://orcid.org/0000-0001-7278-1852>),
Gesmira Molla
[aut] (<https://orcid.org/0000-0002-8628-5056>),
Andrew Butler
[aut] (<https://orcid.org/0000-0003-3608-0463>),
Tim Stuart [aut]
(<https://orcid.org/0000-0002-3044-0897>),
Madeline Kowalski
[ctb] (<https://orcid.org/0000-0002-5655-7620>),
Saket Choudhary
[ctb] (<https://orcid.org/0000-0001-5202-7633>),
Skylar Li [ctb],
Longda Jiang
[ctb] (<https://orcid.org/0000-0003-4964-6497>),
Jeff Farrell [ctb],
Shiwei Zheng
[ctb] (<https://orcid.org/0000-0001-6682-6743>),
Christoph Hafemeister
[ctb]
(<https://orcid.org/0000-0001-6365-8254>),
Patrick Roelli [ctb] |
| Maintainer: |
Rahul Satija <seurat at nygenome.org> |
| BugReports: |
https://github.com/satijalab/seurat-object/issues |
| License: |
MIT + file LICENSE |
| 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, CuratedAtlasQueryR, escape, GeomxTools, mastR, Nebulosa, Platypus, scAnnotate, scaper, sccomp, scCustomize, SCIntRuler, scpoisson, scRepertoire, scRNAseqApp, Signac, SpaNorm, SpatialDecon |
| Reverse suggests: |
cellpypes, CoGAPS, CytoSimplex, DCATS, edgeR, ggsc, MOFA2, mxfda, projectR, RESET, rliger, scDotPlot, scOntoMatch, SCpubr, SFEData, SimBu, singleCellHaystack, singleCellTK, SpatialFeatureExperiment, SpaTopic, SPECK, tidytof, UCell, VAM |
Linking:
Please use the canonical form
https://CRAN.R-project.org/package=SeuratObject
to link to this page.