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DESCRIPTION
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Package: SeuratObject
Title: Data Structures for Single Cell Data
Version: 5.0.99.9004
Authors@R: c(
person(given = 'Paul', family = 'Hoffman', email = '[email protected]', role = 'aut', comment = c(ORCID = '0000-0002-7693-8957')),
person(given = 'Rahul', family = 'Satija', email = '[email protected]', role = c('aut', 'cre'), comment = c(ORCID = '0000-0001-9448-8833')),
person(given = 'David', family = 'Collins', email = '[email protected]', role = 'aut', comment = c(ORCID = '0000-0001-9243-7821')),
person(given = "Yuhan", family = "Hao", email = '[email protected]', role = 'aut', comment = c(ORCID = '0000-0002-1810-0822')),
person(given = "Austin", family = "Hartman", email = '[email protected]', role = 'aut', comment = c(ORCID = '0000-0001-7278-1852')),
person(given = "Gesmira", family = "Molla", email = '[email protected]', role = 'aut', comment = c(ORCID = '0000-0002-8628-5056')),
person(given = 'Andrew', family = 'Butler', email = '[email protected]', role = 'aut', comment = c(ORCID = '0000-0003-3608-0463')),
person(given = 'Tim', family = 'Stuart', email = '[email protected]', role = 'aut', comment = c(ORCID = '0000-0002-3044-0897')),
person(given = "Madeline", family = "Kowalski", email = "[email protected]", role = "ctb", comment = c(ORCID = "0000-0002-5655-7620")),
person(given = "Saket", family = "Choudhary", email = "[email protected]", role = "ctb", comment = c(ORCID = "0000-0001-5202-7633")),
person(given = "Skylar", family = "Li", email = "[email protected]", role = "ctb"),
person(given = "Longda", family = "Jiang", email = "[email protected]", role = "ctb", comment = c(ORCID = "0000-0003-4964-6497")),
person(given = 'Jeff', family = 'Farrell', email = '[email protected]', role = 'ctb'),
person(given = 'Shiwei', family = 'Zheng', email = '[email protected]', role = 'ctb', comment = c(ORCID = '0000-0001-6682-6743')),
person(given = 'Christoph', family = 'Hafemeister', email = '[email protected]', role = 'ctb', comment = c(ORCID = '0000-0001-6365-8254')),
person(given = 'Patrick', family = 'Roelli', email = '[email protected]', role = 'ctb')
)
Description:
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.
License: MIT + file LICENSE
URL:
https://satijalab.github.io/seurat-object/,
https://github.com/satijalab/seurat-object
BugReports:
https://github.com/satijalab/seurat-object/issues
Additional_repositories:
https://bnprks.r-universe.dev
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
Suggests:
BPCells,
DelayedArray,
fs (>= 1.5.2),
ggplot2,
HDF5Array,
rmarkdown,
sf (>= 1.0.0),
testthat
LinkingTo: Rcpp, RcppEigen
Enhances: Seurat
Config/Needs/website: pkgdown
BuildManual: true
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.3.1
Collate:
'RcppExports.R'
'zzz.R'
'generics.R'
'keymixin.R'
'graph.R'
'default.R'
'assay.R'
'logmap.R'
'layers.R'
'assay5.R'
'centroids.R'
'command.R'
'compliance.R'
'data.R'
'jackstraw.R'
'dimreduc.R'
'segmentation.R'
'molecules.R'
'spatial.R'
'fov.R'
'neighbor.R'
'seurat.R'
'sparse.R'
'utils.R'