SPIAT
This is the released version of SPIAT; for the devel version, see SPIAT.
Spatial Image Analysis of Tissues
Bioconductor version: Release (3.23)
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 <yuzhou0610 at gmail.com>
citation("SPIAT")):Anna Trigos, Yuzhou Feng, Tianpei Yang, Mabel Li, John Zhu, Volkan Ozcoban, Maria Doyle. SPIAT: Spatial Image Analysis of Tissues. doi:10.18129/B9.bioc.SPIAT, R package version 1.14.0, https://bioconductor.org/packages/SPIAT.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") 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")| Basic analyses with SPIAT | HTML | R Script |
| Quantifying cell colocalisation with SPIAT | HTML | R Script |
| Reading in data and data formatting in SPIAT | HTML | R Script |
| Identifying cellular neighborhood with SPIAT | HTML | R Script |
| Quality control and visualisation with SPIAT | HTML | R Script |
| Spatial heterogeneity with SPIAT | HTML | R Script |
| Overview of the SPIAT package | HTML | R Script |
| Characterising tissue structure with SPIAT | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | BiomedicalInformatics, CellBiology, Clustering, DataImport, ImmunoOncology, QualityControl, SingleCell, Software, Spatial, Visualization |
| Version | 1.14.0 |
| In Bioconductor since | BioC 3.16 (R-4.2) (4 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 | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | SPIAT_1.14.0.tar.gz |
| Windows Binary (x86_64) | SPIAT_1.14.0.zip |
| macOS Binary (big-sur-x86_64) | SPIAT_1.14.0.tgz |
| macOS Binary (sonoma-arm64) | SPIAT_1.14.0.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 |