spicyR
Spatial analysis of in situ cytometry data
Bioconductor version: Release (3.19)
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]
Maintainer: Ellis Patrick <ellis.patrick at sydney.edu.au>
citation("spicyR")):
Installation
To install this package, start R (version "4.4") 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 | 1.16.4 |
| In Bioconductor since | BioC 3.11 (R-4.0) (4.5 years) |
| License | GPL (>=2) |
| Depends | R (>= 4.1) |
| Imports | ggplot2, concaveman, BiocParallel, spatstat.explore, spatstat.geom, lmerTest, S4Vectors, methods, pheatmap, rlang, grDevices, stats, data.table, dplyr, tidyr, scam, SingleCellExperiment, SpatialExperiment, SummarizedExperiment, ggforce, ClassifyR, tibble, magrittr, cli, extrafont |
| 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 |
| Suggests Me | Statial, spicyWorkflow |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | spicyR_1.16.4.tar.gz |
| Windows Binary (x86_64) | spicyR_1.16.4.zip |
| macOS Binary (x86_64) | spicyR_1.16.3.tgz |
| macOS Binary (arm64) | spicyR_1.16.1.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/spicyR |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/spicyR |
| Bioc Package Browser | https://code.bioconductor.org/browse/spicyR/ |
| Package Short Url | https://bioconductor.org/packages/spicyR/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.19 | Source Archive |