DOI: 10.18129/B9.bioc.SPIAT    

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

Spatial Image Analysis of Tissues

Bioconductor version: Development (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>

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


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HTML R Script Overview of the SPIAT package
PDF   Reference Manual


biocViews BiomedicalInformatics, CellBiology, Clustering, DataImport, ImmunoOncology, QualityControl, SingleCell, Software, Spatial, Visualization
Version 1.1.0
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.core, raster, sp, xROI, elsa, Rtsne, umap, rlang, graphics, SummarizedExperiment
Suggests BiocStyle, knitr, rmarkdown, pkgdown, testthat
URL https://trigosteam.github.io/SPIAT/
BugReports https://github.com/trigosteam/SPIAT/issues
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Source Package SPIAT_1.1.0.tar.gz
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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/
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