Welcome to the new bioconductor.org!

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

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

browseVignettes("microSTASIS")
Introduction to microSTASIS HTML R Script
Reference Manual PDF
NEWS Text

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
See More
Suggests BiocStyle, gghighlight, knitr, rmarkdown, methods, RefManageR, sessioninfo, SingleCellExperiment, SummarizedExperiment, testthat (>= 3.0.0)
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package microSTASIS_1.3.0.tar.gz
Windows Binary
macOS Binary (x86_64) microSTASIS_1.3.0.tgz
macOS Binary (arm64) microSTASIS_1.3.0.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