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combi

Compositional omics model based visual integration

Bioconductor version: Release (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>

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

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

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
Linking To
Suggests knitr, rmarkdown, testthat
System Requirements
Enhances
URL
Bug Reports https://github.com/CenterForStatistics-UGent/combi/issues
See More
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
Old Source Packages for BioC 3.17 Source Archive