spicyR
Spatial analysis of in situ cytometry data
Bioconductor version: 3.23 · Package version: 1.24.0
The spicyR package provides a framework for performing inference on changes in spatial relationships between pairs of cell types for cell-resolution spatial omics technologies. spicyR consists of three primary steps: (i) summarizing the degree of spatial localization between pairs of cell types for each image; (ii) modelling the variability in localization summary statistics as a function of cell counts and (iii) testing for changes in spatial localizations associated with a response variable.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("spicyR")Details
| Maintainer | Ellis Patrick <ellis.patrick@sydney.edu.au> |
| Author | Nicolas Canete [aut], Ellis Patrick [aut, cre], Nicholas Robertson [ctb], Alex Qin [ctb], Farhan Ameen [ctb], Shreya Rao [ctb] |
| License | GPL (>=2) |
| URL | https://ellispatrick.github.io/spicyR/ https://github.com/SydneyBioX/spicyR, https://sydneybiox.github.io/spicyR/ |
| Bug Reports | https://github.com/SydneyBioX/spicyR/issues |
| Downloads rank | 469 |
| Source branch | RELEASE_3_23 |
| biocViews | CellBasedAssays, SingleCell, Software, Spatial |
Documentation
Download
Dependencies
Depends: R (>= 4.1)
Imports: BiocParallel, ClassifyR, S4Vectors, SingleCellExperiment, SpatialExperiment, SummarizedExperiment, cli, concaveman, coxme, data.table, dplyr, ggforce, ggh4x, ggnewscale, ggplot2, ggthemes, grDevices, lifecycle, lmerTest, magrittr, methods, pheatmap, rlang, scales, scam, simpleSeg, spatstat.explore, spatstat.geom, stats, survival, tibble, tidyr
Suggests: SpatialDatasets, BiocStyle, knitr, rmarkdown, pkgdown, imcRtools, testthat (>= 3.0.0)