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Bioconductor - spicyR (development version)

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 (3.22)

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], Nicholas Robertson [ctb], Alex Qin [ctb], Farhan Ameen [ctb], Shreya Rao [ctb]

Maintainer: Ellis Patrick <ellis.patrick at sydney.edu.au>

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

To install this package, start R (version "4.5") 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")
Spatial Linear and Mixed-Effects Modelling with spicy HTML R Script Reference Manual PDF Details biocViews CellBasedAssays, SingleCell, Software, Spatial Version 1.21.2 In Bioconductor since BioC 3.11 (R-4.0) (5 years) License GPL (>=2) Depends R (>= 4.1) Imports ggplot2, concaveman, BiocParallel, spatstat.explore, spatstat.geom, lmerTest, S4Vectors, methods, pheatmap, rlang, grDevices, stats, data.table, dplyr, tidyr, scam, SingleCellExperiment, SpatialExperiment, SummarizedExperiment, ggforce, ClassifyR, tibble, magrittr, cli, survival, ggthemes, ggh4x, coxme, ggnewscale, lifecycle, simpleSeg System Requirements URL https://ellispatrick.github.io/spicyR/https://github.com/SydneyBioX/spicyR https://sydneybiox.github.io/spicyR/ Bug Reports https://github.com/SydneyBioX/spicyR/issues See More Package Archives

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

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