RCM

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

Bioconductor version: Release (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 psb.ugent.be>

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

Installation

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

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DimensionReduction, Metagenomics, Microbiome, Software, Visualization
Version	1.22.0
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
Imports Me
Suggests Me
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	RCM_1.22.0.tar.gz
Windows Binary (x86_64)	RCM_1.22.0.zip
macOS Binary (x86_64)	RCM_1.22.0.tgz
macOS Binary (arm64)	RCM_1.21.0.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