forked from drieslab/Giotto
-
Notifications
You must be signed in to change notification settings - Fork 0
/
DESCRIPTION
155 lines (155 loc) · 3.29 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
150
151
152
153
154
155
Package: Giotto
Title: Spatial Single-Cell Transcriptomics Toolbox
Version: 4.0.0
Authors@R: c(
person("Ruben", "Dries", email = "rubendries@gmail.com",
role = c("aut", "cre")),
person("Jiaji", "George Chen", email = "jiajic@bu.edu",
role = c("aut")),
person("Natalie", "Del Rossi", email = "natalie.delrossi@mssm.edu",
role = c("aut")),
person("Guo-Cheng", "Yuan", email = "guo-cheng.yuan@mssm.edu",
role = c("aut")),
person("Matthew", "O'Brien", email = "mobrien2@bu.edu",
role = c("aut")),
person("Joselyn", "Chávez", email = "joselynchavezf@gmail.com",
role = c("aut"), comment = c(ORCID = "0000-0002-4974-4591"))
)
Maintainer: Ruben Dries <rubendries@gmail.com>
Description: Toolbox to process, analyze and visualize spatial single-cell expression data.
License: GPL (>= 3)
Encoding: UTF-8
LazyData: true
URL: https://drieslab.github.io/Giotto/, https://github.com/drieslab/Giotto
BugReports: https://github.com/drieslab/Giotto/issues
RoxygenNote: 7.2.3
Depends:
base (>= 3.5.0),
utils (>= 3.5.0),
R (>= 3.5.0),
methods,
GiottoUtils,
GiottoClass,
GiottoVisuals
Imports:
BiocParallel,
BiocSingular,
checkmate,
cowplot (>= 0.9.4),
data.table (>= 1.12.2),
dbscan (>= 1.1-3),
future.apply,
ggplot2 (>= 3.1.1),
ggrepel,
grDevices,
graphics,
igraph (>= 1.2.4.1),
jsonlite,
limma,
Matrix,
MatrixGenerics,
plotly,
progressr,
reshape2,
reticulate (>= 1.25),
Rtsne (>= 0.15),
scales (>= 1.0.0),
sparseMatrixStats,
stats,
terra (>= 1.5-12),
uwot (>= 0.0.0.9010)
Suggests:
arrow,
Biobase,
biomaRt,
ClusterR,
clustree,
ComplexHeatmap (>= 1.20.0),
DelayedArray,
DelayedMatrixStats,
dendextend (>= 1.13.0),
dplyr,
exactextractr,
FactoMineR,
factoextra,
fitdistrplus,
FNN,
geometry,
GiottoData,
ggalluvial,
ggdendro,
ggforce,
ggraph,
HDF5Array (>= 1.18.1),
hdf5r,
htmlwidgets,
jackstraw,
knitr,
MAST,
miniUI,
multinet (>= 3.0.2),
networkD3,
png,
quadprog,
harmony,
R.utils,
remotes,
Rfast,
rhdf5,
RTriangle (>= 1.6-0.10),
Rvision,
S4Vectors,
scatterpie,
scattermore,
scran (>= 1.10.1),
Seurat,
sf,
shiny,
SingleCellExperiment,
smfishHmrf,
SPARK,
SpatialExperiment,
spdep,
SummarizedExperiment,
tiff,
trendsceek,
testthat (>= 3.0.0),
qs
Remotes:
drieslab/GiottoUtils,
drieslab/GiottoClass,
drieslab/GiottoVisuals
Collate:
'auxiliary_giotto.R'
'cell_segmentation.R'
'clustering.R'
'convenience.R'
'cross_section.R'
'dd.R'
'differential_expression.R'
'dimension_reduction.R'
'feature_set_enrichment.R'
'general_help.R'
'giotto_viewer.R'
'globals.R'
'suite_reexports.R'
'image_registration.R'
'interactivity.R'
'package_imports.R'
'poly_influence.R'
'python_hmrf.R'
'python_scrublet.R'
'spatial_clusters.R'
'spatial_enrichment.R'
'spatial_enrichment_visuals.R'
'spatial_genes.R'
'spatial_interaction.R'
'spatial_interaction_spot.R'
'spatial_interaction_visuals.R'
'spdep.R'
'variable_genes.R'
'wnn.R'
'zzz.R'
biocViews:
VignetteBuilder: knitr
Config/testthat/edition: 3