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microSTASIS

This is the development version of microSTASIS; for the stable release version, see microSTASIS.

Microbiota STability ASsessment via Iterative cluStering


Bioconductor version: Development (3.19)

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 "4.4") 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

Reference Manual PDF

Details

biocViews BiomedicalInformatics, Clustering, GeneticVariability, Microbiome, MultipleComparison, Software
Version 1.3.0
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
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/microSTASIS
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/microSTASIS
Package Short Url https://bioconductor.org/packages/microSTASIS/
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