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DESCRIPTION
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DESCRIPTION
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Package: Seurat
Version: 5.0.3
Date: 2024-03-18
Title: Tools for Single Cell Genomics
Description: 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.
Authors@R: c(
person(given = "Andrew", family = "Butler", email = "abutler@nygenome.org", role = "ctb", comment = c(ORCID = "0000-0003-3608-0463")),
person(given = "Saket", family = "Choudhary", email = "schoudhary@nygenome.org", role = "ctb", comment = c(ORCID = "0000-0001-5202-7633")),
person(given = "Charlotte", family = "Darby", email = "cdarby@nygenome.org", role = "ctb", comment = c(ORCID = "0000-0003-2195-5300")),
person(given = "Jeff", family = "Farrell", email = "jfarrell@g.harvard.edu", role = "ctb"),
person(given = "Isabella", family = "Grabski", email = "igrabski@nygenome.org", role = "ctb", comment = c(ORCID = "0000-0002-0616-5469")),
person(given = "Christoph", family = "Hafemeister", email = "chafemeister@nygenome.org", role = "ctb", comment = c(ORCID = "0000-0001-6365-8254")),
person(given = "Yuhan", family = "Hao", email = "yhao@nygenome.org", role = "ctb", comment = c(ORCID = "0000-0002-1810-0822")),
person(given = "Austin", family = "Hartman", email = "ahartman@nygenome.org", role = "ctb", comment = c(ORCID = "0000-0001-7278-1852")),
person(given = "Paul", family = "Hoffman", email = "hoff0792@umn.edu", role = "ctb", comment = c(ORCID = "0000-0002-7693-8957")),
person(given = "Jaison", family = "Jain", email = "jjain@nygenome.org", role = "ctb", comment = c(ORCID = "0000-0002-9478-5018")),
person(given = "Longda", family = "Jiang", email = "ljiang@nygenome.org", role = "ctb", comment = c(ORCID = "0000-0003-4964-6497")),
person(given = "Madeline", family = "Kowalski", email = "mkowalski@nygenome.org", role = "ctb", comment = c(ORCID = "0000-0002-5655-7620")),
person(given = "Skylar", family = "Li", email = "sli@nygenome.org", role = "ctb"),
person(given = "Gesmira", family = "Molla", email = 'gmolla@nygenome.org', role = 'ctb', comment = c(ORCID = '0000-0002-8628-5056')),
person(given = "Efthymia", family = "Papalexi", email = "epapalexi@nygenome.org", role = "ctb", comment = c(ORCID = "0000-0001-5898-694X")),
person(given = "Patrick", family = "Roelli", email = "proelli@nygenome.org", role = "ctb"),
person(given = "Rahul", family = "Satija", email = "seurat@nygenome.org", role = c("aut", "cre"), comment = c(ORCID = "0000-0001-9448-8833")),
person(given = "Karthik", family = "Shekhar", email = "kshekhar@berkeley.edu", role = "ctb"),
person(given = "Avi", family = "Srivastava", email = "asrivastava@nygenome.org", role = "ctb", comment = c(ORCID = "0000-0001-9798-2079")),
person(given = "Tim", family = "Stuart", email = "tstuart@nygenome.org", role = "ctb", comment = c(ORCID = "0000-0002-3044-0897")),
person(given = "Kristof", family = "Torkenczy", email = "", role = "ctb", comment = c(ORCID = "0000-0002-4869-7957")),
person(given = "Shiwei", family = "Zheng", email = "szheng@nygenome.org", role = "ctb", comment = c(ORCID = "0000-0001-6682-6743")),
person("Satija Lab and Collaborators", role = "fnd")
)
URL: https://satijalab.org/seurat, https://github.com/satijalab/seurat
BugReports: https://github.com/satijalab/seurat/issues
Additional_repositories: https://satijalab.r-universe.dev, https://bnprks.r-universe.dev
Depends:
R (>= 4.0.0),
methods,
SeuratObject (>= 5.0.0)
Imports:
cluster,
cowplot,
fastDummies,
fitdistrplus,
future,
future.apply,
generics (>= 0.1.3),
ggplot2 (>= 3.3.0),
ggrepel,
ggridges,
graphics,
grDevices,
grid,
httr,
ica,
igraph,
irlba,
jsonlite,
KernSmooth,
leiden (>= 0.3.1),
lifecycle,
lmtest,
MASS,
Matrix (>= 1.5-0),
matrixStats,
miniUI,
patchwork,
pbapply,
plotly (>= 4.9.0),
png,
progressr,
purrr,
RANN,
RColorBrewer,
Rcpp (>= 1.0.7),
RcppAnnoy (>= 0.0.18),
RcppHNSW,
reticulate,
rlang,
ROCR,
RSpectra,
Rtsne,
scales,
scattermore (>= 1.2),
sctransform (>= 0.4.1),
shiny,
spatstat.explore,
spatstat.geom,
stats,
tibble,
tools,
utils,
uwot (>= 0.1.10)
LinkingTo: Rcpp (>= 0.11.0), RcppEigen, RcppProgress
License: MIT + file LICENSE
LazyData: true
Collate:
'RcppExports.R'
'reexports.R'
'generics.R'
'clustering.R'
'visualization.R'
'convenience.R'
'data.R'
'differential_expression.R'
'dimensional_reduction.R'
'integration.R'
'zzz.R'
'integration5.R'
'mixscape.R'
'objects.R'
'preprocessing.R'
'preprocessing5.R'
'roxygen.R'
'sketching.R'
'tree.R'
'utilities.R'
RoxygenNote: 7.3.1
Encoding: UTF-8
Suggests:
ape,
BPCells,
rsvd,
testthat,
hdf5r,
S4Vectors,
SummarizedExperiment,
SingleCellExperiment,
MAST,
DESeq2,
BiocGenerics,
GenomicRanges,
GenomeInfoDb,
IRanges,
rtracklayer,
Rfast2,
monocle,
Biobase,
VGAM,
limma,
metap,
enrichR,
mixtools,
ggrastr,
data.table,
R.utils,
presto,
DelayedArray,
harmony