RCM

DOI: 10.18129/B9.bioc.RCM  

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

Bioconductor version: Release (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>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

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")

 

HTML	R Script	Manual for the RCM pacakage
PDF		Reference Manual
Text		NEWS

Details

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 (>= 2.2.1.9000), nleqslv, phyloseq, tensor, MASS, grDevices, graphics, methods
LinkingTo
Suggests	knitr, rmarkdown, testthat
SystemRequirements
Enhances
URL	https://bioconductor.org/packages/release/bioc/vignettes/RCM/inst/doc/RCMvignette.html/
BugReports	https://github.com/CenterForStatistics-UGent/RCM/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

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/
Package Downloads Report	Download Stats