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Compositional omics model based visual integration

Bioconductor version: Release (3.18)

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 (from within R, enter citation("combi")):


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Manual for the combi pacakage HTML R Script
Reference Manual PDF


biocViews DimensionReduction, Metabolomics, Metagenomics, Microbiome, Software, Visualization
Version 1.14.0
In Bioconductor since BioC 3.11 (R-4.0) (4 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
Bug Reports https://github.com/CenterForStatistics-UGent/combi/issues
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Suggests knitr, rmarkdown, testthat
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Source Package combi_1.14.0.tar.gz
Windows Binary combi_1.14.0.zip
macOS Binary (x86_64) combi_1.14.0.tgz
macOS Binary (arm64) combi_1.14.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/combi
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Bioc Package Browser https://code.bioconductor.org/browse/combi/
Package Short Url https://bioconductor.org/packages/combi/
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