Package: MOFA2
Type: Package
Title: Multi-Omics Factor Analysis v2
Version: 1.20.1
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"))
              )
Date: 2023-01-12
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,
        vizualisation, 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, Seurat, SeuratObject, ggpubr, foreach,
        psych, MultiAssayExperiment, SummarizedExperiment,
        SingleCellExperiment, ggrastr, mvtnorm, GGally, rmarkdown,
        data.table, tidyverse, BiocStyle, Matrix, markdown
biocViews: DimensionReduction, Bayesian, Visualization
URL: https://biofam.github.io/MOFA2/index.html
BugReports: https://github.com/bioFAM/MOFA2
VignetteBuilder: knitr
StagedInstall: no
NeedsCompilation: yes
RoxygenNote: 7.2.3
SystemRequirements: Python (>=3), numpy, pandas, h5py, scipy, argparse,
        sklearn, mofapy2
Config/pak/sysreqs: libicu-dev libpng-dev libssl-dev python3 zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-12-17 13:41:14 UTC
RemoteUrl: https://github.com/bioc/MOFA2
RemoteRef: RELEASE_3_22
RemoteSha: 2d16576b004943eeaa0b29250c59d30e463b2e71
Packaged: 2025-12-18 04:29:40 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>)
Built: R 4.5.2; x86_64-w64-mingw32; 2025-12-18 04:33:08 UTC; windows
