RCM

DOI: 10.18129/B9.bioc.RCM    

This is the development version of RCM; to use it, please install the devel version of Bioconductor.

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

Bioconductor version: Development (3.10)

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>

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

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("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

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 1.1.0
In Bioconductor since BioC 3.9 (R-3.6) (< 6 months)
License GPL-2
Depends
Imports RColorBrewer, alabama, edgeR, reshape2, tseries, vegan, VGAM, ggplot2 (>= 2.2.1.9000), nleqslv, phyloseq, tensor, MASS, stats, grDevices, graphics, methods
LinkingTo
Suggests knitr, rmarkdown, testthat
SystemRequirements
Enhances
URL http://users.ugent.be/~shawinke/RCMmanual/
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_1.1.0.tar.gz
Windows Binary RCM_1.1.0.zip
Mac OS X 10.11 (El Capitan) RCM_1.1.0.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 http://bioconductor.org/packages/RCM/
Package Downloads Report Download Stats

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