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 (3.21)

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: )

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


Reference Manual	PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DimensionReduction, Metagenomics, Microbiome, Software, Visualization
Version	1.23.0
In Bioconductor since	BioC 3.9 (R-3.6) (5.5 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

Suggests	knitr, rmarkdown, testthat
Linking To
Enhances
Depends On Me
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Build Report	Build Report

Package Archives

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

Source Package
Windows Binary (x86_64)	RCM_1.23.0.zip (64-bit only)
macOS Binary (x86_64)	RCM_1.23.0.tgz
macOS Binary (arm64)
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/
Package Downloads Report	Download Stats