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spicyR

This is the development version of spicyR; for the stable release version, see spicyR.

Spatial analysis of in situ cytometry data


Bioconductor version: Development (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]

Maintainer: Ellis Patrick <ellis.patrick at sydney.edu.au>

Citation (from within R, enter citation("spicyR")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")
Introduction to spicy HTML R Script
Reference Manual PDF

Details

biocViews CellBasedAssays, SingleCell, Software, Spatial
Version 1.15.4
In Bioconductor since BioC 3.11 (R-4.0) (4 years)
License GPL (>=2)
Depends R (>= 4.1)
Imports ggplot2, concaveman, BiocParallel, spatstat.explore, spatstat.geom, lmerTest, BiocGenerics, S4Vectors, methods, mgcv, pheatmap, rlang, grDevices, IRanges, stats, data.table, dplyr, tidyr, scam, SingleCellExperiment, SpatialExperiment, SummarizedExperiment, ggforce, ClassifyR, tibble
System Requirements
URL https://ellispatrick.github.io/spicyR/ https://github.com/SydneyBioX/spicyR
Bug Reports https://github.com/SydneyBioX/spicyR/issues
See More
Suggests BiocStyle, knitr, rmarkdown, pkgdown, imcRtools
Linking To
Enhances
Depends On Me
Imports Me lisaClust
Suggests Me spicyWorkflow, Statial
Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package spicyR_1.15.4.tar.gz
Windows Binary spicyR_1.15.4.zip
macOS Binary (x86_64) spicyR_1.15.4.tgz
macOS Binary (arm64) spicyR_1.15.3.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