RCM
This is the development version of RCM; for the stable release version, see RCM.
Fit row-column association models with the negative binomial distribution for the microbiome
DOI: 10.18129/B9.bioc.RCM
Bioconductor version: Development (3.24)
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("RCM")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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")| Manual for the RCM pacakage | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DimensionReduction, Metagenomics, Microbiome, Software, Visualization |
| Version | 1.29.0 |
| In Bioconductor since | BioC 3.9 (R-3.6) (7.5 years) |
| License | GPL-2 |
| Depends | R (>= 4.5.0) |
| 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 | |
| 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_1.29.0.tar.gz |
| Windows Binary (x86_64) | RCM_1.29.0.zip |
| macOS Binary (big-sur-x86_64) | RCM_1.29.0.tgz |
| macOS Binary (sonoma-arm64) | RCM_1.29.0.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 |