spicyR

DOI: 10.18129/B9.bioc.spicyR  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see spicyR.

Spatial analysis of in situ cytometry data

Bioconductor version: 3.17

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>

Installation

To install this package, start R (version "4.3") 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")

 

HTML	R Script	Introduction to spicy
PDF		Reference Manual

Details

biocViews	CellBasedAssays, SingleCell, Software, Spatial
Version	1.12.2
In Bioconductor since	BioC 3.11 (R-4.0) (3.5 years)
License	GPL (>=2)
Depends	R (>= 4.1)
Imports	ggplot2, concaveman, BiocParallel, spatstat.explore, spatstat.geom, lmerTest, BiocGenerics, S4Vectors, lme4, methods, mgcv, pheatmap, rlang, grDevices, IRanges, stats, data.table, dplyr, tidyr, scam, SingleCellExperiment, SpatialExperiment, SummarizedExperiment, ggforce, ClassifyR
LinkingTo
Suggests	BiocStyle, knitr, rmarkdown, pkgdown
SystemRequirements
Enhances
URL	https://ellispatrick.github.io/spicyR/ https://github.com/ellispatrick/spicyR
BugReports	https://github.com/ellispatrick/spicyR/issues
Depends On Me
Imports Me	lisaClust
Suggests Me	spicyWorkflow, Statial
Links To Me
Build Report

Package Archives

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

Source Package	spicyR_1.12.2.tar.gz
Windows Binary	spicyR_1.12.2.zip
macOS Binary (x86_64)	spicyR_1.12.0.tgz
macOS Binary (arm64)	spicyR_1.12.2.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