sosta

This package is for version 3.21 of Bioconductor; for the stable, up-to-date release version, see sosta.

A package for the analysis of anatomical tissue structures in spatial omics data

Bioconductor version: 3.21

sosta (Spatial Omics STructure Analysis) is a package for analyzing spatial omics data to explore tissue organization at the anatomical structure level. It reconstructs anatomically relevant structures based on molecular features or cell types. It further calculates a range of metrics at the structure level to quantitatively describe tissue architecture. The package is designed to integrate with other packages for the analysis of spatial omics data.

Author: Samuel Gunz [aut, cre] ORCID iD ORCID: 0000-0002-8909-0932 , Mark D. Robinson [aut, fnd]

Maintainer: Samuel Gunz <samuel.gunz at uzh.ch>

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

Installation

To install this package, start R (version "4.5") and enter:


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

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("sosta")

Overview of sosta HTML R Script

Reconstruction and analysis of pancreatic islets from IMC data HTML R Script

Reference Manual PDF

NEWS Text

LICENSE Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Software, Spatial, Transcriptomics, Visualization

Version 1.0.1

In Bioconductor since BioC 3.21 (R-4.5) (0.5 years)

License GPL (>= 3) + file LICENSE

Depends R (>= 4.4.0)

Imports terra, sf, smoothr, spatstat.explore, spatstat.geom, SpatialExperiment, SingleCellExperiment, dplyr, ggplot2, patchwork, SummarizedExperiment, stats, rlang, parallel, EBImage, spatstat.random, S4Vectors

System Requirements

URL https://github.com/sgunz/sosta https://sgunz.github.io/sosta/

Bug Reports https://github.com/sgunz/sosta/issues

Suggests knitr, rmarkdown, BiocStyle, ExperimentHub, lme4, lmerTest, ggfortify, tidyr, testthat (>= 3.0.0)

Linking To

Enhances

Depends On Me

Imports Me

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Build Report Build Report

Package Archives

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

Source Package sosta_1.0.1.tar.gz

Windows Binary (x86_64) sosta_1.0.1.zip (64-bit only)

macOS Binary (x86_64) sosta_1.0.1.tgz

macOS Binary (arm64) sosta_1.0.1.tgz

Source Repository git clone https://git.bioconductor.org/packages/sosta

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/sosta

Bioc Package Browser https://code.bioconductor.org/browse/sosta/

Package Short Url https://bioconductor.org/packages/sosta/

Package Downloads Report Download Stats

Old Source Packages for BioC 3.21 Source Archive