microSTASIS

DOI: 10.18129/B9.bioc.microSTASIS  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see microSTASIS.

Microbiota STability ASsessment via Iterative cluStering

Bioconductor version: 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>

Installation

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

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

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	1.0.0
In Bioconductor since	BioC 3.17 (R-4.3) (< 6 months)
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_1.0.0.tar.gz
Windows Binary
macOS Binary (x86_64)	microSTASIS_1.0.0.tgz
macOS Binary (arm64)	microSTASIS_1.0.0.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