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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 (3.18)

spicyR provides a series of functions to aid in the analysis of both immunofluorescence and mass cytometry imaging data as well as other assays that can deeply phenotype individual cells and their spatial location.

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 "4.3") 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 1.13.1
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
Linking To
Suggests BiocStyle, knitr, rmarkdown, pkgdown
System Requirements
Enhances
URL
Bug Reports https://github.com/ellispatrick/spicyR/issues
See More
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_1.13.1.tar.gz
Windows Binary spicyR_1.13.1.zip (64-bit only)
macOS Binary (x86_64) spicyR_1.13.1.tgz
macOS Binary (arm64) spicyR_1.13.1.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