{
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  "Package": "MOFA2",
  "Type": "Package",
  "Title": "Multi-Omics Factor Analysis v2",
  "Version": "1.23.0",
  "Maintainer": "Ricard Argelaguet <ricard.argelaguet@gmail.com>",
  "Authors@R": "c(person(\"Ricard\", \"Argelaguet\", role = c(\"aut\", \"cre\"),\nemail = \"ricard.argelaguet@gmail.com\",\ncomment = c(ORCID = \"http://orcid.org/0000-0003-3199-3722\")),\nperson(\"Damien\", \"Arnol\", role = \"aut\",\nemail = \"damien.arnol@gmail.com\",\ncomment = c(ORCID = \"http://orcid.org/0000-0003-2462-534X\")),\nperson(\"Danila\", \"Bredikhin\", role = \"aut\",\nemail = \"danila.bredikhin@embl.de\",\ncomment = c(ORCID = \"https://orcid.org/0000-0001-8089-6983\")),\nperson(\"Britta\", \"Velten\", role = \"aut\",\nemail = \"britta.velten@gmail.com\",\ncomment = c(ORCID = \"http://orcid.org/0000-0002-8397-3515\"))\n)",
  "Date": "2023-01-12",
  "License": "file LICENSE",
  "Description": "The MOFA2 package contains a collection of tools for\ntraining and analysing multi-omic factor analysis (MOFA). MOFA\nis a probabilistic factor model that aims to identify principal\naxes of variation from data sets that can comprise multiple\nomic layers and/or groups of samples. Additional time or space\ninformation on the samples can be incorporated using the\nMEFISTO framework, which is part of MOFA2. Downstream analysis\nfunctions to inspect molecular features underlying each factor,\nvisualisation, imputation etc are available.",
  "Encoding": "UTF-8",
  "biocViews": "DimensionReduction, Bayesian, Visualization",
  "URL": "https://biofam.github.io/MOFA2/index.html",
  "BugReports": "https://github.com/bioFAM/MOFA2",
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  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:54:07 UTC",
  "RemoteUrl": "https://github.com/bioc/MOFA2",
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  "Packaged": {
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  "Author": "Ricard Argelaguet [aut, cre] (ORCID:\n<https://orcid.org/0000-0003-3199-3722>),\nDamien Arnol [aut] (ORCID: <https://orcid.org/0000-0003-2462-534X>),\nDanila Bredikhin [aut] (ORCID: <https://orcid.org/0000-0001-8089-6983>),\nBritta Velten [aut] (ORCID: <https://orcid.org/0000-0002-8397-3515>)",
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  "_created": "2026-05-30T09:55:14.000Z",
  "_published": "2026-05-30T15:23:51.358Z",
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  "_exports": [
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    "add_mofa_factors_to_seurat",
    "calculate_contribution_scores",
    "calculate_variance_explained",
    "calculate_variance_explained_per_sample",
    "cluster_samples",
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    "covariates_names",
    "covariates_names<-",
    "create_mofa",
    "create_mofa_from_df",
    "create_mofa_from_matrix",
    "create_mofa_from_MultiAssayExperiment",
    "create_mofa_from_Seurat",
    "create_mofa_from_SingleCellExperiment",
    "factors_names",
    "factors_names<-",
    "features_metadata",
    "features_metadata<-",
    "features_names",
    "features_names<-",
    "get_covariates",
    "get_data",
    "get_default_data_options",
    "get_default_mefisto_options",
    "get_default_model_options",
    "get_default_stochastic_options",
    "get_default_training_options",
    "get_dimensions",
    "get_elbo",
    "get_expectations",
    "get_factors",
    "get_group_kernel",
    "get_imputed_data",
    "get_interpolated_factors",
    "get_lengthscales",
    "get_scales",
    "get_variance_explained",
    "get_weights",
    "groups_names",
    "groups_names<-",
    "impute",
    "interpolate_factors",
    "load_model",
    "make_example_data",
    "plot_alignment",
    "plot_ascii_data",
    "plot_data_heatmap",
    "plot_data_overview",
    "plot_data_scatter",
    "plot_data_vs_cov",
    "plot_dimred",
    "plot_enrichment",
    "plot_enrichment_detailed",
    "plot_enrichment_heatmap",
    "plot_factor",
    "plot_factor_cor",
    "plot_factors",
    "plot_factors_vs_cov",
    "plot_group_kernel",
    "plot_interpolation_vs_covariate",
    "plot_sharedness",
    "plot_smoothness",
    "plot_top_weights",
    "plot_variance_explained",
    "plot_variance_explained_by_covariates",
    "plot_variance_explained_per_feature",
    "plot_weights",
    "plot_weights_heatmap",
    "plot_weights_scatter",
    "predict",
    "prepare_mofa",
    "run_enrichment",
    "run_mofa",
    "run_tsne",
    "run_umap",
    "samples_metadata",
    "samples_metadata<-",
    "samples_names",
    "samples_names<-",
    "select_model",
    "set_covariates",
    "subset_factors",
    "subset_features",
    "subset_groups",
    "subset_samples",
    "subset_views",
    "summarise_factors",
    "views_names",
    "views_names<-"
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    {
      "page": "pipe",
      "title": "Re-exporting the pipe operator See 'magrittr::%>%' for details.",
      "topics": [
        "%>%"
      ]
    },
    {
      "page": "add_mofa_factors_to_seurat",
      "title": "Function to add the MOFA representation onto a Seurat object",
      "topics": [
        "add_mofa_factors_to_seurat"
      ]
    },
    {
      "page": "calculate_contribution_scores",
      "title": "Calculate contribution scores for each view in each sample",
      "topics": [
        "calculate_contribution_scores"
      ]
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    {
      "page": "calculate_variance_explained",
      "title": "Calculate variance explained by the model",
      "topics": [
        "calculate_variance_explained"
      ]
    },
    {
      "page": "calculate_variance_explained_per_sample",
      "title": "Calculate variance explained by the MOFA factors for each sample",
      "topics": [
        "calculate_variance_explained_per_sample"
      ]
    },
    {
      "page": "cluster_samples",
      "title": "K-means clustering on samples based on latent factors",
      "topics": [
        "cluster_samples"
      ]
    },
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      "page": "compare_elbo",
      "title": "Compare different trained 'MOFA' objects in terms of the final value of the ELBO statistics and number of inferred factors",
      "topics": [
        "compare_elbo"
      ]
    },
    {
      "page": "compare_factors",
      "title": "Plot the correlation of factors between different models",
      "topics": [
        "compare_factors"
      ]
    },
    {
      "page": "correlate_factors_with_covariates",
      "title": "Plot correlation of factors with external covariates",
      "topics": [
        "correlate_factors_with_covariates"
      ]
    },
    {
      "page": "covariates_names",
      "title": "covariates_names: set and retrieve covariate names",
      "topics": [
        "covariates,MOFA-method",
        "covariates_names",
        "covariates_names,MOFA-method",
        "covariates_names<-",
        "covariates_names<-,MOFA,vector-method"
      ]
    },
    {
      "page": "create_mofa",
      "title": "create a MOFA object",
      "topics": [
        "create_mofa"
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      "page": "create_mofa_from_df",
      "title": "create a MOFA object from a data.frame object",
      "topics": [
        "create_mofa_from_df"
      ]
    },
    {
      "page": "create_mofa_from_matrix",
      "title": "create a MOFA object from a a list of matrices",
      "topics": [
        "create_mofa_from_matrix"
      ]
    },
    {
      "page": "create_mofa_from_MultiAssayExperiment",
      "title": "create a MOFA object from a MultiAssayExperiment object",
      "topics": [
        "create_mofa_from_MultiAssayExperiment"
      ]
    },
    {
      "page": "create_mofa_from_Seurat",
      "title": "create a MOFA object from a Seurat object",
      "topics": [
        "create_mofa_from_Seurat"
      ]
    },
    {
      "page": "create_mofa_from_SingleCellExperiment",
      "title": "create a MOFA object from a SingleCellExperiment object",
      "topics": [
        "create_mofa_from_SingleCellExperiment"
      ]
    },
    {
      "page": "factors_names",
      "title": "factors_names: set and retrieve factor names",
      "topics": [
        "factors_names",
        "factors_names,MOFA-method",
        "factors_names<-",
        "factors_names<-,MOFA,vector-method"
      ]
    },
    {
      "page": "features_metadata",
      "title": "features_metadata: set and retrieve feature metadata",
      "topics": [
        "features_metadata",
        "features_metadata,MOFA-method",
        "features_metadata<-",
        "features_metadata<-,MOFA,data.frame-method"
      ]
    },
    {
      "page": "features_names",
      "title": "features_names: set and retrieve feature names",
      "topics": [
        "features_names",
        "features_names,MOFA-method",
        "features_names<-",
        "features_names<-,MOFA,list-method"
      ]
    },
    {
      "page": "get_covariates",
      "title": "Get sample covariates",
      "topics": [
        "get_covariates"
      ]
    },
    {
      "page": "get_data",
      "title": "Get data",
      "topics": [
        "get_data"
      ]
    },
    {
      "page": "get_default_data_options",
      "title": "Get default data options",
      "topics": [
        "get_default_data_options"
      ]
    },
    {
      "page": "get_default_mefisto_options",
      "title": "Get default options for MEFISTO covariates",
      "topics": [
        "get_default_mefisto_options"
      ]
    },
    {
      "page": "get_default_model_options",
      "title": "Get default model options",
      "topics": [
        "get_default_model_options"
      ]
    },
    {
      "page": "get_default_stochastic_options",
      "title": "Get default stochastic options",
      "topics": [
        "get_default_stochastic_options"
      ]
    },
    {
      "page": "get_default_training_options",
      "title": "Get default training options",
      "topics": [
        "get_default_training_options"
      ]
    },
    {
      "page": "get_dimensions",
      "title": "Get dimensions",
      "topics": [
        "get_dimensions"
      ]
    },
    {
      "page": "get_elbo",
      "title": "Get ELBO",
      "topics": [
        "get_elbo"
      ]
    },
    {
      "page": "get_expectations",
      "title": "Get expectations",
      "topics": [
        "get_expectations"
      ]
    },
    {
      "page": "get_factors",
      "title": "Get factors",
      "topics": [
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      "page": "get_group_kernel",
      "title": "Get group covariance matrix",
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      "page": "get_interpolated_factors",
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      "page": "plot_dimred",
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      "page": "plot_enrichment",
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      "page": "plot_variance_explained_by_covariates",
      "title": "Plot variance explained by the smooth components of the model",
      "topics": [
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      "page": "plot_variance_explained_per_feature",
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