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DESCRIPTION
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Package: STutility
Type: Package
Title: Analysis and visualization of Spatial Transcriptomics data
Version: 1.1.1
Authors@R:
c(person(
"Ludvig", "Larsson",
email = "[email protected]",
role = c("aut", "cre")
),
person(
"Joseph", "Bergenstraahle",
role = c("aut")
))
Description: STutility collects useful tools for Spatial Transcriptomics data analysis within R.
The package is built on top of popular Seurat R package, which is a toolkit for analysis and exploration of single cell RNA sequencing data (scRNAseq).
STutility adds image functionallity to the Seurat workflow, allowing RNAseq data to be put in a spatial tissue context.
Tutorials for data transformation, QC, analysis and visualization can be found on our website: https://ludvigla.github.io/STUtility_web_site/.
License: MIT + file LICENSE
Encoding: UTF-8
Depends:
Seurat (>= 3.0.0),
ggplot2 (>= 3.2.0)
Imports:
methods,
cowplot,
dplyr,
purrr,
zeallot,
magrittr,
jsonlite,
igraph (>= 1.2.4),
plotly (>= 4.9.0),
Matrix (>= 1.2),
imager (>= 0.41),
shiny (>= 1.3.0),
raster (>= 3.0),
magick (>= 2.0),
scales (>= 1.0.0),
data.table (>= 1.12.2),
reshape2 (>= 1.4.3),
patchwork,
shinyjs
Suggests:
knitr,
rmarkdown,
reticulate,
sp (>= 1.3),
spData (>= 0.3.2),
dbscan (>= 1.1),
RColorBrewer,
ggiraph (>= 0.6),
viridis (>= 0.5.0),
Morpho (>= 2.7),
Rvcg (>= 0.18),
tibble,
ica (>= 1.0),
irlba (>= 2.3.3),
akima (>= 0.6),
spdep (>= 1.1),
spatstat.explore,
spatstat.model,
NNLM
VignetteBuilder: knitr
RoxygenNote: 7.2.3
Collate:
'2D_point_pattern.R'
'3D_viusalization.R'
'HSVencoding.R'
'Image_resolution_switch.R'
'Mask_functions.R'
'QC.R'
'RegionNeighbours.R'
'Rigid_transformation.R'
'generics.R'
'Staffli.R'
'RunNMF.R'
'Spatial_genes.R'
'Visualization_utilities.R'
'Visualization.R'
'crop_utilities.R'
'facet_grid_SC.R'
'image_processing_utilities.R'
'image_processing.R'
'manual_annotation.R'
'pre_processing.R'
'process_from_table.R'
'utilities.R'