Files in MOFA2

Multi-Omics Factor Analysis v2

README.md R/load_model.R R/imports.R R/AllGenerics.R R/basilisk.R R/utils.R R/calculate_variance_explained.R R/get_methods.R R/enrichment.R R/QC.R R/plot_data.R R/dimensionality_reduction.R R/prepare_mofa.R R/plot_factors.R R/plot_weights.R R/impute.R R/make_example_data.R R/AllClasses.R R/subset.R R/run_mofa.R R/compare_models.R R/create_mofa.R R/set_methods.R R/predict.R R/cluster_samples.R R/correlate_covariates.R vignettes/downstream_analysis.Rmd vignettes/getting_started_R.Rmd man/select_model.Rd man/create_mofa_from_matrix.Rd man/create_mofa.Rd man/plot_factor_cor.Rd man/summarise_factors.Rd man/plot_variance_explained_per_feature.Rd man/plot_enrichment.Rd man/samples_names.Rd man/subset_features.Rd man/plot_factor.Rd man/run_mofa.Rd man/calculate_variance_explained.Rd man/get_imputed_data.Rd man/plot_variance_explained.Rd man/correlate_factors_with_covariates.Rd man/compare_elbo.Rd man/get_data.Rd man/get_default_model_options.Rd man/get_factors.Rd man/get_dimensions.Rd man/create_mofa_from_MultiAssayExperiment.Rd man/pipe.Rd man/subset_views.Rd man/create_mofa_from_df.Rd man/plot_weights.Rd man/get_expectations.Rd man/compare_factors.Rd man/subset_groups.Rd man/plot_factors.Rd man/plot_enrichment_heatmap.Rd man/predict.Rd man/get_variance_explained.Rd man/get_default_training_options.Rd man/plot_weights_heatmap.Rd man/factors_names.Rd man/subset_factors.Rd man/run_tsne.Rd man/MOFA.Rd man/subset_samples.Rd man/run_umap.Rd man/features_names.Rd man/plot_weights_scatter.Rd man/create_mofa_from_Seurat.Rd man/plot_data_overview.Rd man/prepare_mofa.Rd man/get_elbo.Rd man/impute.Rd man/make_example_data.Rd man/load_model.Rd man/run_enrichment.Rd man/cluster_samples.Rd man/plot_enrichment_detailed.Rd man/samples_metadata.Rd man/get_default_stochastic_options.Rd man/get_default_data_options.Rd man/plot_data_scatter.Rd man/get_weights.Rd man/plot_ascii_data.Rd man/views_names.Rd man/groups_names.Rd man/plot_data_heatmap.Rd man/features_metadata.Rd man/create_mofa_from_SingleCellExperiment.Rd man/plot_dimred.Rd man/plot_top_weights.Rd tests/testthat.R tests/testthat/test_plot.R tests/testthat/test_create_model.R tests/testthat/test_prepare_model.R tests/testthat/test_load_model.R inst/doc/downstream_analysis.Rmd inst/doc/downstream_analysis.R inst/doc/getting_started_R.R inst/doc/getting_started_R.Rmd inst/scripts/template_script.R