Revision 21bb473e8a8f34f4fa192c651ec462cef2f9b1a3 authored by David Collins on 10 May 2024, 11:18:33 UTC, committed by David Collins on 10 May 2024, 11:23:47 UTC
1 parent a9ce48f
DESCRIPTION
Package: Seurat
Version: 5.1.0
Date: 2024-05-08
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 = 'David', family = 'Collins', email = 'dcollins@nygenome.org', role = 'ctb', comment = c(ORCID = '0000-0001-9243-7821')),
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 (>= 5.0.2)
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,
arrow,
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
![swh spinner](/static/img/swh-spinner.gif)
Computing file changes ...