spicyR
This is the released version of spicyR; for the devel version, see spicyR.
Spatial analysis of in situ cytometry data
Bioconductor version: Release (3.23)
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.
Author: Nicolas Canete [aut], Ellis Patrick [aut, cre], Nicholas Robertson [ctb], Alex Qin [ctb], Farhan Ameen [ctb], Shreya Rao [ctb]
Maintainer: Ellis Patrick <ellis.patrick at sydney.edu.au>
citation("spicyR")):Nicolas Canete, Ellis Patrick. spicyR: Spatial analysis of in situ cytometry data. doi:10.18129/B9.bioc.spicyR, R package version 1.24.0, https://bioconductor.org/packages/spicyR.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("spicyR")For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("spicyR")| "Spatial Linear and Mixed-Effects Modelling with spicy" | HTML | R Script |
| Reference Manual |
Details
| biocViews | CellBasedAssays, SingleCell, Software, Spatial |
| Version | 1.24.0 |
| In Bioconductor since | BioC 3.11 (R-4.0) (6.5 years) |
| License | GPL (>=2) |
| 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 |
| System Requirements | |
| URL | https://ellispatrick.github.io/spicyR/ https://github.com/SydneyBioX/spicyR https://sydneybiox.github.io/spicyR/ |
| Bug Reports | https://github.com/SydneyBioX/spicyR/issues |
See More
| Suggests | SpatialDatasets, BiocStyle, knitr, rmarkdown, pkgdown, imcRtools, testthat (>= 3.0.0) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | lisaClust, OSTA |
| Suggests Me | Statial |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | spicyR_1.24.0.tar.gz |
| Windows Binary (x86_64) | spicyR_1.24.0.zip |
| macOS Binary (big-sur-x86_64) | spicyR_1.24.0.tgz |
| macOS Binary (sonoma-arm64) | spicyR_1.24.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/spicyR |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/spicyR |
| Package Short Url | https://bioconductor.org/packages/spicyR/ |
| Package Downloads Report | Download Stats |