sosta
This is the development version of sosta; for the stable release version, see sosta.
A package for the analysis of anatomical tissue structures in spatial omics data
Bioconductor version: Development (3.24)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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")| 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 | 1.5.1 |
| In Bioconductor since | BioC 3.21 (R-4.5) (1.5 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_1.5.1.tar.gz |
| Windows Binary (x86_64) | sosta_1.5.1.zip |
| macOS Binary (big-sur-x86_64) | sosta_1.5.1.tgz |
| macOS Binary (sonoma-arm64) | sosta_1.5.1.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 |