DOI: 10.18129/B9.bioc.RCM  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see RCM.

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

Bioconductor version: 3.16

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]

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

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


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biocViews DimensionReduction, Metagenomics, Microbiome, Software, Visualization
Version 1.14.0
In Bioconductor since BioC 3.9 (R-3.6) (4 years)
License GPL-2
Depends R (>= 4.0), DBI
Imports RColorBrewer, alabama, edgeR, reshape2, tseries, stats, VGAM, ggplot2 (>=, nleqslv, phyloseq, tensor, MASS, grDevices, graphics, methods
Suggests knitr, rmarkdown, testthat
URL https://bioconductor.org/packages/release/bioc/vignettes/RCM/inst/doc/RCMvignette.html/
BugReports https://github.com/CenterForStatistics-UGent/RCM/issues
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Source Package RCM_1.14.0.tar.gz
Windows Binary RCM_1.14.0.zip
macOS Binary (x86_64) RCM_1.14.0.tgz
macOS Binary (arm64) RCM_1.14.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/RCM
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/RCM
Bioc Package Browser https://code.bioconductor.org/browse/RCM/
Package Short Url https://bioconductor.org/packages/RCM/
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