combi

DOI: 10.18129/B9.bioc.combi  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see combi.

Compositional omics model based visual integration

Bioconductor version: 3.17

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>

Installation

To install this package, start R (version "4.3") 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")

 

HTML	R Script	Manual for the combi pacakage
PDF		Reference Manual
Text		NEWS

Details

biocViews	DimensionReduction, Metabolomics, Metagenomics, Microbiome, Software, Visualization
Version	1.12.1
In Bioconductor since	BioC 3.11 (R-4.0) (3.5 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
LinkingTo
Suggests	knitr, rmarkdown, testthat
SystemRequirements
Enhances
URL
BugReports	https://github.com/CenterForStatistics-UGent/combi/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	combi_1.12.1.tar.gz
Windows Binary	combi_1.12.1.zip
macOS Binary (x86_64)	combi_1.12.1.tgz
macOS Binary (arm64)	combi_1.12.0.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