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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 (3.20)

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>

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


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


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

Manual for the RCM pacakage HTML R Script
Reference Manual PDF


biocViews DimensionReduction, Metagenomics, Microbiome, Software, Visualization
Version 1.21.0
In Bioconductor since BioC 3.9 (R-3.6) (5 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
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Source Package RCM_1.21.0.tar.gz
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