SPIAT

DOI: 10.18129/B9.bioc.SPIAT  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see SPIAT.

Spatial Image Analysis of Tissues

Bioconductor version: 3.17

SPIAT (**Sp**atial **I**mage **A**nalysis of **T**issues) is an R package with a suite of data processing, quality control, visualization and data analysis tools. SPIAT is compatible with data generated from single-cell spatial proteomics platforms (e.g. OPAL, CODEX, MIBI, cellprofiler). SPIAT reads spatial data in the form of X and Y coordinates of cells, marker intensities and cell phenotypes. SPIAT includes six analysis modules that allow visualization, calculation of cell colocalization, categorization of the immune microenvironment relative to tumor areas, analysis of cellular neighborhoods, and the quantification of spatial heterogeneity, providing a comprehensive toolkit for spatial data analysis.

Author: Anna Trigos [aut] , Yuzhou Feng [aut, cre] , Tianpei Yang [aut], Mabel Li [aut], John Zhu [aut], Volkan Ozcoban [aut], Maria Doyle [aut]

Maintainer: Yuzhou Feng <yuzhou.feng at petermac.org>

Installation

To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("SPIAT")

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("SPIAT")

 

HTML	R Script	Basic analyses with SPIAT
HTML	R Script	Characterising tissue structure with SPIAT
HTML	R Script	Identifying cellular neighborhood with SPIAT
HTML	R Script	Overview of the SPIAT package
HTML	R Script	Quality control and visualisation with SPIAT
HTML	R Script	Quantifying cell colocalisation with SPIAT
HTML	R Script	Reading in data and data formatting in SPIAT
HTML	R Script	Spatial heterogeneity with SPIAT
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	BiomedicalInformatics, CellBiology, Clustering, DataImport, ImmunoOncology, QualityControl, SingleCell, Software, Spatial, Visualization
Version	1.2.3
In Bioconductor since	BioC 3.16 (R-4.2) (1 year)
License	Artistic-2.0
Depends	R (>= 4.2.0), SpatialExperiment(>= 1.8.0)
Imports	apcluster (>= 1.4.7), ggplot2 (>= 3.2.1), gridExtra (>= 2.3), gtools (>= 3.8.1), reshape2 (>= 1.4.3), dplyr (>= 0.8.3), RANN (>= 2.6.1), pracma (>= 2.2.5), dbscan (>= 1.1-5), mmand (>= 1.5.4), tibble (>= 2.1.3), grDevices, stats, utils, vroom, dittoSeq, spatstat.geom, methods, spatstat.explore, raster, sp, SummarizedExperiment, rlang
LinkingTo
Suggests	BiocStyle, plotly (>= 4.9.0), knitr, rmarkdown, pkgdown, testthat, graphics, alphahull, Rtsne, umap, ComplexHeatmap, elsa
SystemRequirements
Enhances
URL	https://trigosteam.github.io/SPIAT/
BugReports	https://github.com/trigosteam/SPIAT/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	SPIAT_1.2.3.tar.gz
Windows Binary	SPIAT_1.2.3.zip
macOS Binary (x86_64)	SPIAT_1.2.3.tgz
macOS Binary (arm64)	SPIAT_1.2.3.tgz
Source Repository	git clone https://git.bioconductor.org/packages/SPIAT
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/SPIAT
Bioc Package Browser	https://code.bioconductor.org/browse/SPIAT/
Package Short Url	https://bioconductor.org/packages/SPIAT/
Package Downloads Report	Download Stats