MOFA
This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.
This package is for version 3.12 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see MOFA (see replacement MOFA2).
Multi-Omics Factor Analysis (MOFA)
Bioconductor version: 3.12
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 gmail.com>
citation("MOFA")):
Installation
To install this package, start R (version "4.0") and enter:
if (!require("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")| 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 assess model robustness and do model selection | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Bayesian, DimensionReduction, Software, Visualization |
| Version | 1.6.2 |
| In Bioconductor since | BioC 3.9 (R-3.6) (5 years) |
| 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 |
| System Requirements | Python (>=2.7.0), numpy, pandas, h5py, scipy, sklearn, mofapy |
| URL |
See More
| Suggests | knitr, MOFAdata |
| 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 | MOFA_1.6.2.tar.gz |
| Windows Binary | MOFA_1.6.2.zip |
| macOS 10.13 (High Sierra) | MOFA_1.6.2.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 |
| Old Source Packages for BioC 3.12 | Source Archive |