-
Notifications
You must be signed in to change notification settings - Fork 920
/
DESCRIPTION
149 lines (149 loc) · 5.65 KB
/
DESCRIPTION
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
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 = "[email protected]", role = "ctb", comment = c(ORCID = "0000-0003-3608-0463")),
person(given = "Saket", family = "Choudhary", email = "[email protected]", role = "ctb", comment = c(ORCID = "0000-0001-5202-7633")),
person(given = 'David', family = 'Collins', email = '[email protected]', role = 'ctb', comment = c(ORCID = '0000-0001-9243-7821')),
person(given = "Charlotte", family = "Darby", email = "[email protected]", role = "ctb", comment = c(ORCID = "0000-0003-2195-5300")),
person(given = "Jeff", family = "Farrell", email = "[email protected]", role = "ctb"),
person(given = "Isabella", family = "Grabski", email = "[email protected]", role = "ctb", comment = c(ORCID = "0000-0002-0616-5469")),
person(given = "Christoph", family = "Hafemeister", email = "[email protected]", role = "ctb", comment = c(ORCID = "0000-0001-6365-8254")),
person(given = "Yuhan", family = "Hao", email = "[email protected]", role = "ctb", comment = c(ORCID = "0000-0002-1810-0822")),
person(given = "Austin", family = "Hartman", email = "[email protected]", role = "ctb", comment = c(ORCID = "0000-0001-7278-1852")),
person(given = "Paul", family = "Hoffman", email = "[email protected]", role = "ctb", comment = c(ORCID = "0000-0002-7693-8957")),
person(given = "Jaison", family = "Jain", email = "[email protected]", role = "ctb", comment = c(ORCID = "0000-0002-9478-5018")),
person(given = "Longda", family = "Jiang", email = "[email protected]", role = "ctb", comment = c(ORCID = "0000-0003-4964-6497")),
person(given = "Madeline", family = "Kowalski", email = "[email protected]", role = "ctb", comment = c(ORCID = "0000-0002-5655-7620")),
person(given = "Skylar", family = "Li", email = "[email protected]", role = "ctb"),
person(given = "Gesmira", family = "Molla", email = '[email protected]', role = 'ctb', comment = c(ORCID = '0000-0002-8628-5056')),
person(given = "Efthymia", family = "Papalexi", email = "[email protected]", role = "ctb", comment = c(ORCID = "0000-0001-5898-694X")),
person(given = "Patrick", family = "Roelli", email = "[email protected]", role = "ctb"),
person(given = "Rahul", family = "Satija", email = "[email protected]", role = c("aut", "cre"), comment = c(ORCID = "0000-0001-9448-8833")),
person(given = "Karthik", family = "Shekhar", email = "[email protected]", role = "ctb"),
person(given = "Avi", family = "Srivastava", email = "[email protected]", role = "ctb", comment = c(ORCID = "0000-0001-9798-2079")),
person(given = "Tim", family = "Stuart", email = "[email protected]", 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 = "[email protected]", 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