RCM

DOI: 10.18129/B9.bioc.RCM    

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

Bioconductor version: Release (3.13)

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.

Author: Stijn Hawinkel <stijn.hawinkel at ugent.be>

Maintainer: Joris Meys <joris.meys at ugent.be>

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("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	1.8.0
In Bioconductor since	BioC 3.9 (R-3.6) (2.5 years)
License	GPL-2
Depends	R (>= 3.6.0)
Imports	RColorBrewer, alabama, edgeR, reshape2, tseries, VGAM, ggplot2 (>= 2.2.1.9000), nleqslv, phyloseq, tensor, MASS, stats, 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_1.8.0.tar.gz
Windows Binary	RCM_1.8.0.zip
macOS 10.13 (High Sierra)	RCM_1.8.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/RCM
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/RCM
Package Short Url	https://bioconductor.org/packages/RCM/
Package Downloads Report	Download Stats