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SPIAT

This is the development version of SPIAT; for the stable release version, see SPIAT.

Spatial Image Analysis of Tissues


Bioconductor version: Development (3.19)

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>

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

Installation

To install this package, start R (version "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")
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 HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews BiomedicalInformatics, CellBiology, Clustering, DataImport, ImmunoOncology, QualityControl, SingleCell, Software, Spatial, Visualization
Version 1.5.2
In Bioconductor since BioC 3.16 (R-4.2) (1.5 years)
License Artistic-2.0 + file LICENSE
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
System Requirements
URL https://trigosteam.github.io/SPIAT/
Bug Reports https://github.com/trigosteam/SPIAT/issues
See More
Suggests BiocStyle, plotly (>= 4.9.0), knitr, rmarkdown, pkgdown, testthat, graphics, alphahull, Rtsne, umap, ComplexHeatmap, elsa
Linking To
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Package Archives

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

Source Package SPIAT_1.5.2.tar.gz
Windows Binary SPIAT_1.5.2.zip
macOS Binary (x86_64) SPIAT_1.5.2.tgz
macOS Binary (arm64) SPIAT_1.5.2.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