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Microbiota STability ASsessment via Iterative cluStering

Bioconductor version: Release (3.18)

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")):


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

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

Introduction to microSTASIS HTML R Script
Reference Manual PDF


biocViews BiomedicalInformatics, Clustering, GeneticVariability, Microbiome, MultipleComparison, Software
Version 1.2.0
In Bioconductor since BioC 3.17 (R-4.3) (1 year)
License GPL-3
Depends R (>= 4.2.0)
Imports BiocParallel, ggplot2, ggside, grid, rlang, stats, stringr, TreeSummarizedExperiment
System Requirements
URL https://doi.org/10.1093/bib/bbac055
Bug Reports https://github.com/BiotechPedro/microSTASIS
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Suggests BiocStyle, gghighlight, knitr, rmarkdown, methods, RefManageR, sessioninfo, SingleCellExperiment, SummarizedExperiment, testthat (>= 3.0.0)
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Package Archives

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

Source Package microSTASIS_1.2.0.tar.gz
Windows Binary
macOS Binary (x86_64) microSTASIS_1.2.0.tgz
macOS Binary (arm64) microSTASIS_1.2.0.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/
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