Registration Open for Bioc2024
Early registration discount pricing ends May 31!

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 (3.20)

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]

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 1.17.1
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, S4Vectors, methods, pheatmap, rlang, grDevices, stats, data.table, dplyr, tidyr, scam, SingleCellExperiment, SpatialExperiment, SummarizedExperiment, ggforce, ClassifyR, tibble, magrittr, cli
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, testthat (>= 3.0.0)
Linking To
Enhances
Depends On Me
Imports Me lisaClust
Suggests Me Statial
Links To Me
Build Report Build Report

Package Archives

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

Source Package spicyR_1.17.1.tar.gz
Windows Binary spicyR_1.17.1.zip
macOS Binary (x86_64) spicyR_1.17.1.tgz
macOS Binary (arm64) spicyR_1.17.1.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