Statial

DOI: 10.18129/B9.bioc.Statial  

A package to identify changes in cell state relative to spatial associations

Bioconductor version: Release (3.17)

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], Shila Ghazanfar [aut], Ellis Patrick [aut]

Maintainer: Farhan Ameen <fame2827 at uni.sydney.edu.au>

Installation

To install this package, start R (version "4.3") and enter:

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

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")

 

HTML	R Script	Introduction to Statial
PDF		Reference Manual

Details

biocViews	Classification, SingleCell, Software, Spatial
Version	1.2.4
In Bioconductor since	BioC 3.16 (R-4.2) (1 year)
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
LinkingTo
Suggests	BiocStyle, knitr, testthat (>= 3.0.0), ClassifyR, spicyR, ggsurvfit, lisaClust, survival
SystemRequirements
Enhances
URL	https://sydneybiox.github.io/Statial https://github.com/SydneyBioX/Statial/issues
BugReports	https://github.com/SydneyBioX/Statial/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	Statial_1.2.4.tar.gz
Windows Binary	Statial_1.2.4.zip
macOS Binary (x86_64)	Statial_1.2.4.tgz
macOS Binary (arm64)	Statial_1.2.4.tgz
Source Repository	git clone https://git.bioconductor.org/packages/Statial
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/Statial
Bioc Package Browser	https://code.bioconductor.org/browse/Statial/
Package Short Url	https://bioconductor.org/packages/Statial/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.17	Source Archive