Package: MOFA2
Type: Package
Title: Multi-Omics Factor Analysis v2
Version: 1.23.2
Maintainer: Ricard Argelaguet <ricard.argelaguet@gmail.com>
Authors@R: c(person("Ricard", "Argelaguet", role = c("aut", "cre"),
                     email = "ricard.argelaguet@gmail.com",
                     comment = c(ORCID = "http://orcid.org/0000-0003-3199-3722")),
              person("Damien", "Arnol", role = "aut",
                     email = "damien.arnol@gmail.com",
                     comment = c(ORCID = "http://orcid.org/0000-0003-2462-534X")),
              person("Danila", "Bredikhin", role = "aut",
                     email = "danila.bredikhin@embl.de",
                     comment = c(ORCID = "https://orcid.org/0000-0001-8089-6983")),                     
              person("Britta", "Velten", role = "aut",
              		email = "britta.velten@gmail.com",
              		comment = c(ORCID = "http://orcid.org/0000-0002-8397-3515"))
              )
License: file LICENSE
Description: 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,
        visualisation, imputation etc are available.
Encoding: UTF-8
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
Suggests: knitr, testthat (>= 3.0.0), Seurat, SeuratObject, ggpubr,
        foreach, psych, SingleCellExperiment, ggrastr, mvtnorm, GGally,
        rmarkdown, data.table, tidyverse, BiocStyle, Matrix, markdown,
        mia, MOFAdata, MultiAssayExperiment, SummarizedExperiment
biocViews: DimensionReduction, Bayesian, Visualization
URL: https://biofam.github.io/MOFA2/index.html
BugReports: https://github.com/bioFAM/MOFA2
VignetteBuilder: knitr
StagedInstall: no
NeedsCompilation: yes
SystemRequirements: Python (>=3), numpy, pandas, h5py, scipy, argparse,
        sklearn, mofapy2
Config/roxygen2/version: 8.0.0
Config/testthat/edition: 3
Config/pak/sysreqs: libicu-dev libpng-dev libssl-dev python3 zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-08-26 13:21:02 UTC
RemoteUrl: https://github.com/bioc/MOFA2
RemoteRef: HEAD
RemoteSha: 4a102f2b491ab600738ddf693a70f0baf032ca68
Packaged: 2026-09-25 12:09:48 UTC; root
Author: Ricard Argelaguet [aut, cre] (ORCID:
    <https://orcid.org/0000-0003-3199-3722>),
  Damien Arnol [aut] (ORCID: <https://orcid.org/0000-0003-2462-534X>),
  Danila Bredikhin [aut] (ORCID: <https://orcid.org/0000-0001-8089-6983>),
  Britta Velten [aut] (ORCID: <https://orcid.org/0000-0002-8397-3515>)