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Bioconductor - MOFA2 (development version)

MOFA2

This is the development version of MOFA2; for the stable release version, see MOFA2.

Multi-Omics Factor Analysis v2

Bioconductor version: Development (3.22)

The MOFA2 package contains a collection of tools for training and analysing multi-omic factor analysis (MOFA). MOFA is a probabilistic factor model that aims to identify principal axes of variation from data sets that can comprise multiple omic layers and/or groups of samples. Additional time or space information on the samples can be incorporated using the MEFISTO framework, which is part of MOFA2. Downstream analysis functions to inspect molecular features underlying each factor, vizualisation, imputation etc are available.

Author: Ricard Argelaguet [aut, cre] ORCID: 0000-0003-3199-3722 , Damien Arnol [aut] ORCID: 0000-0003-2462-534X , Danila Bredikhin [aut] ORCID: 0000-0001-8089-6983 , Britta Velten [aut] ORCID: 0000-0002-8397-3515

Maintainer: Ricard Argelaguet <ricard.argelaguet at gmail.com>

Citation (from within R, enter citation("MOFA2")): Installation

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


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("MOFA2")

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("MOFA2")

Details biocViews Bayesian, DimensionReduction, Software, Visualization Version 1.19.0 In Bioconductor since BioC 3.12 (R-4.0) (4.5 years) License file LICENSE Depends R (>= 4.0) Imports rhdf5, dplyr, tidyr, reshape2, pheatmap, ggplot2, methods, RColorBrewer, cowplot, ggrepel, reticulate, HDF5Array, grDevices, stats, magrittr, forcats, utils, corrplot, DelayedArray, Rtsne, uwot, basilisk, stringi System Requirements Python (>=3), numpy, pandas, h5py, scipy, argparse, sklearn, mofapy2 URL https://biofam.github.io/MOFA2/index.html Bug Reports https://github.com/bioFAM/MOFA2 See More Suggests knitr, testthat, Seurat, SeuratObject, ggpubr, foreach, psych, MultiAssayExperiment, SummarizedExperiment, SingleCellExperiment, ggrastr, mvtnorm, GGally, rmarkdown, data.table, tidyverse, BiocStyle, Matrix, markdown Linking To Enhances Depends On Me Imports Me RFLOMICS Suggests Me HoloFoodR, SUMO Links To Me Build Report Build Report Package Archives

Follow Installation instructions to use this package in your R session.

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