DOI: 10.18129/B9.bioc.spicyR  

Spatial analysis of in situ cytometry data

Bioconductor version: Release (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>

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 1.12.2
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
Suggests BiocStyle, knitr, rmarkdown, pkgdown
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

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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
Old Source Packages for BioC 3.17 Source Archive

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