SPIAT
This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see SPIAT.
Spatial Image Analysis of Tissues
Bioconductor version: 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("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")| 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 | ||
| NEWS | Text |
Details
| biocViews | BiomedicalInformatics, CellBiology, Clustering, DataImport, ImmunoOncology, QualityControl, SingleCell, Software, Spatial, Visualization |
| Version | 1.0.4 |
| In Bioconductor since | BioC 3.16 (R-4.2) (1.5 years) |
| 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, elsa, Rtsne, umap, rlang, graphics, SummarizedExperiment |
| System Requirements | |
| URL | https://trigosteam.github.io/SPIAT/ |
| Bug Reports | https://github.com/trigosteam/SPIAT/issues |
See More
| Suggests | BiocStyle, knitr, rmarkdown, pkgdown, testthat, xROI |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | SPIAT_1.0.4.tar.gz |
| Windows Binary | SPIAT_1.0.4.zip |
| macOS Binary (x86_64) | SPIAT_1.0.4.tgz |
| macOS Binary (arm64) | SPIAT_1.0.4.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 |
| Old Source Packages for BioC 3.16 | Source Archive |