combi

This package is for version 3.21 of Bioconductor; for the stable, up-to-date release version, see combi.

Compositional omics model based visual integration

Bioconductor version: 3.21

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] ORCID iD ORCID: 0000-0002-4501-5180

Maintainer: Stijn Hawinkel <stijn.hawinkel at psb.ugent.be>

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

Installation

To install this package, start R (version "4.5") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews DimensionReduction, Metabolomics, Metagenomics, Microbiome, Software, Visualization

Version 1.20.0

In Bioconductor since BioC 3.11 (R-4.0) (5.5 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

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_1.20.0.tar.gz

Windows Binary (x86_64) combi_1.20.0.zip

macOS Binary (x86_64) combi_1.20.0.tgz

macOS Binary (arm64) combi_1.20.0.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