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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 (3.19)

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>

Citation (from within R, enter citation("Statial")):

Installation

To install this package, start R (version "4.4") and enter:


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

# The following initializes usage of Bioc devel
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 PDF

Details

biocViews Classification, SingleCell, Software, Spatial
Version 1.5.5
In Bioconductor since BioC 3.16 (R-4.2) (1.5 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
System Requirements
URL https://sydneybiox.github.io/Statial https://github.com/SydneyBioX/Statial/issues
Bug Reports https://github.com/SydneyBioX/Statial/issues
See More
Suggests BiocStyle, knitr, testthat (>= 3.0.0), ClassifyR, spicyR, ggsurvfit, lisaClust, survival
Linking To
Enhances
Depends On Me
Imports Me
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Build Report Build Report

Package Archives

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

Source Package Statial_1.5.5.tar.gz
Windows Binary Statial_1.5.5.zip
macOS Binary (x86_64) Statial_1.5.5.tgz
macOS Binary (arm64) Statial_1.5.5.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