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DESCRIPTION
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DESCRIPTION
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Package: Giotto
Title: Spatial Single-Cell Transcriptomics Toolbox
Version: 4.1.5
Authors@R: c(
person("Ruben", "Dries", email = "rubendries@gmail.com",
role = c("aut", "cre"), comment = c(ORCID = "0000-0001-7650-7754")),
person("Jiaji", "George Chen", email = "jiajic@bu.edu",
role = c("aut")),
person("Joselyn C.", "Chávez-Fuentes", email = "joselynchavezf@gmail.com",
role = c("aut"), comment = c(ORCID = "0000-0002-4974-4591")),
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("Edward", "Ruiz", email = "ecruiz@bu.edu",
role = c("aut")),
person("Wen", "Wang", email = "wen.wang@mssm.edu",
role = c("aut")),
person("Natalie", "Del Rossi", email = "natalie.delrossi@mssm.edu",
role = c("aut"))
)
Description: Toolbox to process, analyze and visualize spatial single-cell expression data.
License: MIT + file LICENSE
Encoding: UTF-8
URL: https://drieslab.github.io/Giotto/, https://github.com/drieslab/Giotto
BugReports: https://github.com/drieslab/Giotto/issues
RoxygenNote: 7.3.2
Depends:
R (>= 4.4.1),
methods,
GiottoClass (>= 0.4.1)
Imports:
BiocParallel,
BiocSingular,
checkmate,
data.table (>= 1.12.2),
dbscan (>= 1.1-3),
ggraph,
ggplot2 (>= 3.1.1),
GiottoUtils (>= 0.2.0),
GiottoVisuals (>= 0.2.6),
igraph (>= 1.2.4.1),
Matrix (>= 1.6-2),
MatrixGenerics,
reticulate (>= 1.25),
scales (>= 1.0.0),
sparseMatrixStats,
stats,
terra (>= 1.7-39),
uwot (>= 0.0.0.9010)
Suggests:
ArchR,
arrow,
biomaRt,
ClusterR,
clustree,
ComplexHeatmap (>= 1.20.0),
DelayedArray,
DelayedMatrixStats,
dendextend (>= 1.13.0),
dplyr,
FactoMineR,
factoextra,
fitdistrplus,
FNN,
future,
future.apply,
GiottoData,
ggalluvial,
ggdendro,
ggforce,
ggspavis,
graphcoloring,
HDF5Array (>= 1.18.1),
hdf5r,
kableExtra,
knitr,
limma,
MAST,
miniUI,
multinet (>= 3.0.2),
networkD3,
pheatmap,
plotly,
quadprog,
harmony,
R.utils,
remotes,
Rfast,
rlang,
rhdf5,
RTriangle (>= 1.6-0.10),
Rtsne (>= 0.15),
Rvision,
scater,
scran (>= 1.10.1),
Seurat,
sf,
shiny,
SingleCellExperiment,
smfishHmrf,
SPARK,
SpatialExperiment,
spdep,
STexampleData,
SummarizedExperiment,
tidygraph,
trendsceek,
testthat (>= 3.0.0),
rmarkdown
Remotes:
drieslab/GiottoUtils,
drieslab/GiottoClass,
drieslab/GiottoVisuals
Collate:
'ONTraC_wrapper.R'
'auxiliary_giotto.R'
'cell_segmentation.R'
'clustering.R'
'convenience_cosmx.R'
'convenience_general.R'
'convenience_visiumHD.R'
'convenience_xenium.R'
'cross_section.R'
'dd.R'
'differential_expression.R'
'dimension_reduction.R'
'feature_set_enrichment.R'
'filter.R'
'general_help.R'
'giotto_viewer.R'
'globals.R'
'gstop.R'
'suite_reexports.R'
'image_registration.R'
'interactivity.R'
'kriging.R'
'normalize.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: Software, Technology, Spatial, SingleCell, Transcriptomics
VignetteBuilder: knitr
Config/testthat/edition: 3