SPIAT

DOI: 10.18129/B9.bioc.SPIAT    

Spatial Image Analysis of Tissues

Bioconductor version: Release (3.16)

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 "4.2") 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 Overview of the SPIAT package
PDF   Reference Manual
Text   NEWS

Details

biocViews BiomedicalInformatics, CellBiology, Clustering, DataImport, ImmunoOncology, QualityControl, SingleCell, Software, Spatial, Visualization
Version 1.0.2
In Bioconductor since BioC 3.16 (R-4.2) (< 6 months)
License Artistic-2.0
Depends R (>= 4.2.0), SpatialExperiment
Imports apcluster (>= 1.4.7), ggplot2 (>= 3.2.1), gridExtra (>= 2.3), gtools (>= 3.8.1), reshape2 (>= 1.4.3), dplyr (>= 0.8.3), plotly (>= 4.9.0), RANN (>= 2.6.1), pracma (>= 2.2.5), dbscan (>= 1.1-5), mmand (>= 1.5.4), tibble (>= 2.1.3), grDevices, stats, utils, vroom, ComplexHeatmap, dittoSeq, spatstat.geom, alphahull, methods, spatstat.explore, raster, sp, xROI, elsa, Rtsne, umap, rlang, graphics, SummarizedExperiment
LinkingTo
Suggests BiocStyle, knitr, rmarkdown, pkgdown, testthat
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_1.0.2.tar.gz
Windows Binary SPIAT_1.0.2.zip
macOS Binary (x86_64) SPIAT_1.0.2.tgz
macOS Binary (arm64) SPIAT_1.0.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/SPIAT
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/SPIAT
Package Short Url https://bioconductor.org/packages/SPIAT/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.16 Source Archive

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