sosta
This is the released version of sosta; for the devel version, see sosta.
A package for the analysis of anatomical tissue structures in spatial omics data
Bioconductor version: Release (3.22)
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]
, Mark D. Robinson [aut, fnd]
Maintainer: Samuel Gunz <samuel.gunz at uzh.ch>
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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Software, Spatial, Transcriptomics, Visualization |
| Version | 1.2.0 |
| 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 |
See More
| Suggests | knitr, rmarkdown, BiocStyle, ExperimentHub, lme4, lmerTest, ggfortify, tidyr, testthat (>= 3.0.0) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | OSTA |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | sosta_1.2.0.tar.gz |
| Windows Binary (x86_64) | sosta_1.1.1.zip |
| macOS Binary (x86_64) | sosta_1.2.0.tgz |
| macOS Binary (arm64) | sosta_1.2.0.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 |