sosta
This is the development version of sosta; to use it, please install the devel version of Bioconductor.
A package for the analysis of anatomical tissue structures in spatial omics data
Bioconductor version: Development (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 morphologically relevant structures based on molecular features or cell types. It further calculates a range of structural and shape metrics 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:
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")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
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")| 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 | 0.99.3 |
| In Bioconductor since | BioC 3.21 (R-4.5) |
| License | GPL (>= 3) + file LICENSE |
| Depends | R (>= 4.4.0) |
| Imports | terra, sf, smoothr, spatstat.explore, spatstat.geom, SpatialExperiment, dplyr, ggplot2, patchwork, SummarizedExperiment, stats, rlang, parallel |
| 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, ggspavis, BiocStyle, imcdatasets, ggfortify, tidyr, testthat (>= 3.0.0) |
| 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 | sosta_0.99.3.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | sosta_0.99.3.tgz |
| macOS Binary (arm64) | sosta_0.99.3.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 |