combi
Compositional omics model based visual integration
Bioconductor version: Release (3.19)
This explorative ordination method combines quasi-likelihood estimation, compositional regression models and latent variable models for integrative visualization of several omics datasets. Both unconstrained and constrained integration are available. The results are shown as interpretable, compositional multiplots.
Author: Stijn Hawinkel [cre, aut] 
Maintainer: Stijn Hawinkel <stijn.hawinkel at psb.ugent.be>
citation("combi")):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("combi")
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("combi")| Manual for the combi pacakage | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DimensionReduction, Metabolomics, Metagenomics, Microbiome, Software, Visualization |
| Version | 1.16.0 |
| In Bioconductor since | BioC 3.11 (R-4.0) (4.5 years) |
| License | GPL-2 |
| Depends | R (>= 4.0), DBI |
| Imports | ggplot2, nleqslv, phyloseq, tensor, stats, limma, Matrix (>= 1.6.0), BB, reshape2, alabama, cobs, Biobase, vegan, grDevices, graphics, methods, SummarizedExperiment |
| System Requirements | |
| URL | |
| Bug Reports | https://github.com/CenterForStatistics-UGent/combi/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 | combi_1.16.0.tar.gz |
| Windows Binary (x86_64) | combi_1.16.0.zip |
| macOS Binary (x86_64) | combi_1.16.0.tgz |
| macOS Binary (arm64) | combi_1.16.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/combi |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/combi |
| Bioc Package Browser | https://code.bioconductor.org/browse/combi/ |
| Package Short Url | https://bioconductor.org/packages/combi/ |
| Package Downloads Report | Download Stats |