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Showing content from https://www.bioconductor.org/packages/devel/bioc/html/../../bioc/html/../../bioc/html/RCM.html below:

Bioconductor - RCM (development version)

RCM

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

Fit row-column association models with the negative binomial distribution for the microbiome

Bioconductor version: Development (3.22)

Combine ideas of log-linear analysis of contingency table, flexible response function estimation and empirical Bayes dispersion estimation for explorative visualization of microbiome datasets. The package includes unconstrained as well as constrained analysis. In addition, diagnostic plot to detect lack of fit are available.

Author: Stijn Hawinkel [cre, aut] ORCID: 0000-0002-4501-5180

Maintainer: Stijn Hawinkel <stijn.hawinkel at psb.ugent.be>

Citation (from within R, enter citation("RCM")): 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("RCM")

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("RCM")
Details biocViews DimensionReduction, Metagenomics, Microbiome, Software, Visualization Version 1.25.0 In Bioconductor since BioC 3.9 (R-3.6) (6 years) License GPL-2 Depends R (>= 4.0), DBI Imports RColorBrewer, alabama, edgeR, reshape2, tseries, stats, VGAM, ggplot2 (>= 2.2.1.9000), nleqslv, phyloseq, tensor, MASS, grDevices, graphics, methods System Requirements URL https://bioconductor.org/packages/release/bioc/vignettes/RCM/inst/doc/RCMvignette.html/ Bug Reports https://github.com/CenterForStatistics-UGent/RCM/issues See More Package Archives

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

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