RCM
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see RCM.
Fit row-column association models with the negative binomial distribution for the microbiome
Bioconductor version: 3.9
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("RCM")):
Installation
To install this package, start R (version "3.6") 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 | ||
| NEWS | Text |
Details
| biocViews | DimensionReduction, Metagenomics, Microbiome, Software, Visualization |
| Version | 1.0.0 |
| In Bioconductor since | BioC 3.9 (R-3.6) (5 years) |
| 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 |
| System Requirements | |
| URL | http://users.ugent.be/~shawinke/RCMmanual/ |
| Bug Reports | https://github.com/CenterForStatistics-UGent/RCM/issues |
See More
| 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_1.0.0.tar.gz |
| Windows Binary | RCM_1.0.0.zip (32- & 64-bit) |
| Mac OS X 10.11 (El Capitan) | RCM_1.0.0.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 |
| Old Source Packages for BioC 3.9 | Source Archive |