microSTASIS

DOI: 10.18129/B9.bioc.microSTASIS    

This is the development version of microSTASIS; to use it, please install the devel version of Bioconductor.

Microbiota STability ASsessment via Iterative cluStering

Bioconductor version: Development (3.17)

The toolkit 'µSTASIS', or microSTASIS, has been developed for the stability analysis of microbiota in a temporal framework by leveraging on iterative clustering. Concretely, the core function uses Hartigan-Wong k-means algorithm as many times as possible for stressing out paired samples from the same individuals to test if they remain together for multiple numbers of clusters over a whole data set of individuals. Moreover, the package includes multiple functions to subset samples from paired times, validate the results or visualize the output.

Author: Pedro Sánchez-Sánchez [aut, cre] , Alfonso Benítez-Páez [aut]

Maintainer: Pedro Sánchez-Sánchez <bio.pedro.technology at gmail.com>

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

Installation

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

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("microSTASIS")

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("microSTASIS")

 

HTML R Script Introduction to microSTASIS
PDF   Reference Manual
Text   NEWS

Details

biocViews BiomedicalInformatics, Clustering, GeneticVariability, Microbiome, MultipleComparison, Software
Version 0.99.2
In Bioconductor since BioC 3.17 (R-4.3)
License GPL-3
Depends R (>= 4.2.0)
Imports BiocParallel, ggplot2, ggside, grid, rlang, stats, stringr, TreeSummarizedExperiment
LinkingTo
Suggests BiocStyle, gghighlight, knitr, rmarkdown, methods, RefManageR, sessioninfo, SingleCellExperiment, SummarizedExperiment, testthat (>= 3.0.0)
SystemRequirements
Enhances
URL https://doi.org/10.1093/bib/bbac055
BugReports https://github.com/BiotechPedro/microSTASIS
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 microSTASIS_0.99.2.tar.gz
Windows Binary
macOS Binary (x86_64) microSTASIS_0.99.2.tgz
macOS Binary (arm64) microSTASIS_0.99.2.tgz
Source Repository git clone https://git.bioconductor.org/packages/microSTASIS
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/microSTASIS
Bioc Package Browser https://code.bioconductor.org/browse/microSTASIS/
Package Short Url https://bioconductor.org/packages/microSTASIS/
Package Downloads Report Download Stats

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