MOFA

DOI: 10.18129/B9.bioc.MOFA    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see MOFA.

Multi-Omics Factor Analysis (MOFA)

Bioconductor version: 3.9

Multi-Omics Factor Analysis: an unsupervised framework for the integration of multi-omics data sets.

Author: Ricard Argelaguet, Britta Velten, Damien Arnol, Florian Buettner, Wolfgang Huber, Oliver Stegle

Maintainer: Britta Velten <britta.velten at embl.de>

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("MOFA")

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("MOFA")

 

HTML	R Script	Introduction to MOFA
HTML	R Script	MOFA: Application to a single-cell multi-omics data set
HTML	R Script	MOFA: applications to a multi-omics data set of CLL patients
HTML	R Script	MOFA: How to do assess model robustness and do model selection
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	Bayesian, DimensionReduction, Software, Visualization
Version	1.0.0
In Bioconductor since	BioC 3.9 (R-3.6) (< 6 months)
License	LGPL-3 | file LICENSE
Depends	R (>= 3.5)
Imports	rhdf5, dplyr, reshape2, pheatmap, corrplot, ggplot2, ggbeeswarm, methods, scales, GGally, RColorBrewer, cowplot, ggrepel, MultiAssayExperiment, Biobase, doParallel, foreach, reticulate, grDevices, stats, utils
LinkingTo
Suggests	knitr, MOFAdata
SystemRequirements	Python (>=2.7.0), numpy, pandas, h5py, scipy, sklearn, mofapy
Enhances
URL
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	MOFA_1.0.0.tar.gz
Windows Binary	MOFA_1.0.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	MOFA_1.0.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/MOFA
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/MOFA
Package Short Url	https://bioconductor.org/packages/MOFA/
Package Downloads Report	Download Stats