microSTASIS
This is the development version of microSTASIS; for the stable release version, see microSTASIS.
Microbiota STability ASsessment via Iterative cluStering
Bioconductor version: Development (3.21)
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] (ORCID:
Maintainer: Pedro Sánchez-Sánchez <bio.pedro.technology at gmail.com>
citation("microSTASIS")):
Installation
To install this package, start R (version "4.5") 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 | ||
| NEWS | Text |
Details
| biocViews | BiomedicalInformatics, Clustering, GeneticVariability, Microbiome, MultipleComparison, Software |
| Version | 1.7.0 |
| In Bioconductor since | BioC 3.17 (R-4.3) (1.5 years) |
| 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_1.7.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | microSTASIS_1.7.0.tgz |
| macOS Binary (arm64) | microSTASIS_1.7.0.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 |