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>

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

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")
Introduction to SegmentedCells HTML R Script
Introduction to spicy HTML R Script
Reference Manual PDF

Details

biocViews CellBasedAssays, SingleCell, Software
Version 1.6.0
In Bioconductor since BioC 3.11 (R-4.0) (4 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
System Requirements
URL
Bug Reports https://github.com/ellispatrick/spicyR/issues
See More
Suggests BiocStyle, knitr, rmarkdown
Linking To
Enhances
Depends On Me
Imports Me lisaClust
Suggests Me
Links To Me
Build Report 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
Bioc Package Browser https://code.bioconductor.org/browse/spicyR/
Package Short Url https://bioconductor.org/packages/spicyR/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.14 Source Archive