Statial
This is the development version of Statial; for the stable release version, see Statial.
A package to identify changes in cell state relative to spatial associations
Bioconductor version: Development (3.24)
Statial is a suite of functions for identifying changes in cell state. The functionality provided by Statial provides robust quantification of cell type localisation which are invariant to changes in tissue structure. In addition to this Statial uncovers changes in marker expression associated with varying levels of localisation. These features can be used to explore how the structure and function of different cell types may be altered by the agents they are surrounded with.
Author: Farhan Ameen [aut, cre], Sourish Iyengar [aut], Alex Qin [aut], Shila Ghazanfar [aut], Ellis Patrick [aut]
Maintainer: Farhan Ameen <fame2827 at uni.sydney.edu.au>
citation("Statial")):Farhan Ameen, Sourish Iyengar, Alex Qin, Shila Ghazanfar, Ellis Patrick. Statial: A package to identify changes in cell state relative to spatial associations. doi:10.18129/B9.bioc.Statial, R package version 1.15.3, https://bioconductor.org/packages/Statial.
Generated from the package metadata; it may differ from the package's own citation.
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("Statial")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("Statial")| "Introduction to Statial" | HTML | R Script |
| Reference Manual |
Details
| biocViews | Classification, SingleCell, Software, Spatial |
| Version | 1.15.3 |
| In Bioconductor since | BioC 3.16 (R-4.2) (4 years) |
| License | GPL-3 |
| Depends | R (>= 4.1.0) |
| Imports | BiocParallel, spatstat.geom, concaveman, data.table, spatstat.explore, dplyr, tidyr, SingleCellExperiment, tibble, stringr, tidyselect, ggplot2, methods, stats, SummarizedExperiment, S4Vectors, plotly, purrr, ranger, magrittr, limma, SpatialExperiment, cluster, treekoR, edgeR, spicyR (>= 1.99.3), Rcpp |
| System Requirements | |
| URL | https://sydneybiox.github.io/Statial https://github.com/SydneyBioX/Statial/issues https://sydneybiox.github.io/Statial/ |
| Bug Reports | https://github.com/SydneyBioX/Statial/issues |
See More
| Suggests | BiocStyle, knitr, testthat (>= 3.0.0), ClassifyR, ggsurvfit, lisaClust, survival |
| Linking To | Rcpp |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | OSTA |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | Statial_1.15.3.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | Statial_1.15.3.tgz |
| macOS Binary (sonoma-arm64) | Statial_1.15.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/Statial |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/Statial |
| Package Short Url | https://bioconductor.org/packages/Statial/ |
| Package Downloads Report | Download Stats |