Files in bioFAM/MOFA2
Multi-Omics Factor Analysis v2
.Rbuildignore
.gitattributes
.gitignore
.gitmodules
DESCRIPTION
Dockerfile
LICENSE
MOFA2.Rproj
NAMESPACE
R/AllClasses.R
R/AllGenerics.R
R/QC.R
R/basilisk.R
R/calculate_variance_explained.R
R/cluster_samples.R
R/compare_models.R
R/contribution_scores.R
R/correlate_covariates.R
R/create_mofa.R
R/dimensionality_reduction.R
R/enrichment.R
R/get_methods.R
R/imports.R
R/impute.R
R/load_model.R
R/make_example_data.R
R/mefisto.R
R/plot_data.R
R/plot_factors.R
R/plot_weights.R
R/predict.R
R/prepare_mofa.R
R/run_mofa.R
R/set_methods.R
R/subset.R
R/utils.R
README.md
configure
configure.win
inst/CITATION
inst/extdata/MEFISTO_model.hdf5
inst/extdata/model.hdf5
inst/extdata/test_data.RData
inst/scripts/template_script.R
inst/scripts/template_script.py
inst/scripts/template_script_dataframe.py
inst/scripts/template_script_matrix.py
man/.Rapp.history
man/MOFA.Rd
man/add_mofa_factors_to_seurat.Rd
man/calculate_contribution_scores.Rd
man/calculate_variance_explained.Rd
man/calculate_variance_explained_per_sample.Rd
man/cluster_samples.Rd
man/compare_elbo.Rd
man/compare_factors.Rd
man/correlate_factors_with_covariates.Rd
man/covariates_names.Rd
man/create_mofa.Rd
man/create_mofa_from_MultiAssayExperiment.Rd
man/create_mofa_from_Seurat.Rd
man/create_mofa_from_SingleCellExperiment.Rd
man/create_mofa_from_df.Rd
man/create_mofa_from_matrix.Rd
man/factors_names.Rd
man/features_metadata.Rd
man/features_names.Rd
man/get_covariates.Rd
man/get_data.Rd
man/get_default_data_options.Rd
man/get_default_mefisto_options.Rd
man/get_default_model_options.Rd
man/get_default_stochastic_options.Rd
man/get_default_training_options.Rd
man/get_dimensions.Rd
man/get_elbo.Rd
man/get_expectations.Rd
man/get_factors.Rd
man/get_group_kernel.Rd
man/get_imputed_data.Rd
man/get_interpolated_factors.Rd
man/get_lengthscales.Rd
man/get_scales.Rd
man/get_variance_explained.Rd
man/get_weights.Rd
man/groups_names.Rd
man/impute.Rd
man/interpolate_factors.Rd
man/load_model.Rd
man/make_example_data.Rd
man/pipe.Rd
man/plot_alignment.Rd
man/plot_ascii_data.Rd
man/plot_data_heatmap.Rd
man/plot_data_overview.Rd
man/plot_data_scatter.Rd
man/plot_data_vs_cov.Rd
man/plot_dimred.Rd
man/plot_enrichment.Rd
man/plot_enrichment_detailed.Rd
man/plot_enrichment_heatmap.Rd
man/plot_factor.Rd
man/plot_factor_cor.Rd
man/plot_factors.Rd
man/plot_factors_vs_cov.Rd
man/plot_group_kernel.Rd
man/plot_interpolation_vs_covariate.Rd
man/plot_sharedness.Rd
man/plot_smoothness.Rd
man/plot_top_weights.Rd
man/plot_variance_explained.Rd
man/plot_variance_explained_by_covariates.Rd
man/plot_variance_explained_per_feature.Rd
man/plot_weights.Rd
man/plot_weights_heatmap.Rd
man/plot_weights_scatter.Rd
man/predict.Rd
man/prepare_mofa.Rd
man/run_enrichment.Rd
man/run_mofa.Rd
man/run_tsne.Rd
man/run_umap.Rd
man/samples_metadata.Rd
man/samples_names.Rd
man/select_model.Rd
man/set_covariates.Rd
man/subset_factors.Rd
man/subset_features.Rd
man/subset_groups.Rd
man/subset_samples.Rd
man/subset_views.Rd
man/summarise_factors.Rd
man/views_names.Rd
setup.py
tests/testthat.R
tests/testthat/barcodes.tsv
tests/testthat/genes.tsv
tests/testthat/matrix.csv
tests/testthat/matrix.mtx
tests/testthat/test_create_model.R
tests/testthat/test_load_model.R
tests/testthat/test_plot.R
tests/testthat/test_prepare_model.R
vignettes/MEFISTO_temporal.Rmd
vignettes/downstream_analysis.Rmd
vignettes/getting_started_R.Rmd
