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
bioFAM/MOFA2 documentation built on June 12, 2024, 3:57 p.m.