DOI: 10.18129/B9.bioc.spicyR  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see spicyR.

Spatial analysis of in situ cytometry data

Bioconductor version: 3.16

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")):


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HTML R Script Introduction to spicy
PDF   Reference Manual


biocViews CellBasedAssays, SingleCell, Software, Spatial
Version 1.10.7
In Bioconductor since BioC 3.11 (R-4.0) (3 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
Suggests BiocStyle, knitr, rmarkdown, pkgdown
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_1.10.7.tar.gz
Windows Binary spicyR_1.10.7.zip
macOS Binary (x86_64) spicyR_1.10.7.tgz
macOS Binary (arm64) spicyR_1.10.7.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/
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