spicyR

DOI: 10.18129/B9.bioc.spicyR    

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see spicyR.

Spatial analysis of in situ cytometry data

Bioconductor version: 3.14

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>

Installation

To install this package, start R (version "4.1") 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 SegmentedCells
HTML	R Script	Introduction to spicy
PDF		Reference Manual

Details

biocViews	CellBasedAssays, SingleCell, Software
Version	1.6.0
In Bioconductor since	BioC 3.11 (R-4.0) (2 years)
License	GPL (>=2)
Depends	R (>= 4.1)
Imports	ggplot2, concaveman, BiocParallel, spatstat.core, spatstat.geom, lmerTest, BiocGenerics, S4Vectors, lme4, methods, mgcv, pheatmap, rlang, grDevices, IRanges, stats, data.table, dplyr, tidyr, scam
LinkingTo
Suggests	BiocStyle, knitr, rmarkdown
SystemRequirements
Enhances
URL
BugReports	https://github.com/ellispatrick/spicyR/issues
Depends On Me
Imports Me	lisaClust
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	spicyR_1.6.0.tar.gz
Windows Binary	spicyR_1.6.0.zip
macOS 10.13 (High Sierra)	spicyR_1.6.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/spicyR
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/spicyR
Package Short Url	https://bioconductor.org/packages/spicyR/
Package Downloads Report	Download Stats