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RCM

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


Bioconductor version: Release (3.18)

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 "4.3") 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

Details

biocViews DimensionReduction, Metagenomics, Microbiome, Software, Visualization
Version 1.18.0
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 (>= 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
See More
Suggests knitr, rmarkdown, testthat
Linking To
Enhances
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Build Report Build Report

Package Archives

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

Source Package RCM_1.18.0.tar.gz
Windows Binary RCM_1.18.0.zip (64-bit only)
macOS Binary (x86_64) RCM_1.18.0.tgz
macOS Binary (arm64) RCM_1.18.0.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