Files in saezlab/cosmosR
COSMOS (Causal Oriented Search of Multi-Omic Space)
.Rbuildignore
.github/.gitignore
.github/workflows/check-bioc.yml
.gitignore
DESCRIPTION
LICENSE
NAMESPACE
NEWS.md
R/HMDB_mapper_vec.R
R/binarize_with_sign.R
R/check_COSMOS_inputs.R
R/check_gene_names.R
R/check_inputs_CARNIVAL.R
R/check_network_data_coverage.R
R/compress_same_children.R
R/cosmos_data.R
R/decoupleRnival.R
R/default_CARNIVAL_options.R
R/discretize_vector.R
R/display_node_neighboorhood.R
R/filter_input_nodes_not_in_pkn.R
R/filter_pkn_expressed_genes.R
R/filter_transcriptional_regulations.R
R/format_COSMOS_results.R
R/get_TF_activity_from_CARNIVAL.R
R/keep_downstream_neighbours.R
R/limit_string_vec.R
R/load_tf_regulon_dorothea.R
R/meta_network.R
R/prepare_metab_inputs.R
R/preprocess_COSMOS.R
R/preprocess_COSMOS_metabolism_to_signaling.R
R/preprocess_COSMOS_signaling_to_metabolism.R
R/process_CARNIVAL_results.R
R/runCARNIVAL_wrapper.R
R/run_COSMOS_metabolism_to_signaling.R
R/run_COSMOS_signaling_to_metabolism.R
R/support_ORA.R
R/support_decoupleR.R
R/support_pheatmap.R
R/sysdata.rda
R/toy_RNA.R
R/toy_metabolic_input.R
R/toy_network.R
R/toy_signaling_input.R
README.md
data/HMDB_mapper_vec.RData
data/meta_network.RData
data/toy_RNA.RData
data/toy_metabolic_input.RData
data/toy_network.RData
data/toy_signaling_input.RData
inst/CITATION
man/HMDB_mapper_vec.Rd
man/compress_same_children.Rd
man/cosmos_data.Rd
man/createLinearColors.Rd
man/decompress_moon_result.Rd
man/decompress_solution_network.Rd
man/decoupleRnival.Rd
man/default_CARNIVAL_options.Rd
man/display_node_neighboorhood.Rd
man/extract_nodes_for_ORA.Rd
man/figures/graphical_abstract.png
man/figures/intro_data.png
man/figures/logo.png
man/figures/summary.png
man/filter_incohrent_TF_target.Rd
man/format_COSMOS_res.Rd
man/format_LR_ressource.Rd
man/get_moon_scoring_network.Rd
man/gmt_to_dataframe.Rd
man/load_tf_regulon_dorothea.Rd
man/make_heatmap_color_palette.Rd
man/meta_network.Rd
man/meta_network_cleanup.Rd
man/moon.Rd
man/prepare_metab_inputs.Rd
man/preprocess_COSMOS_metabolism_to_signaling.Rd
man/preprocess_COSMOS_signaling_to_metabolism.Rd
man/print.cosmos_data.Rd
man/reduce_solution_network.Rd
man/run_COSMOS_metabolism_to_signaling.Rd
man/run_COSMOS_signaling_to_metabolism.Rd
man/toy_RNA.Rd
man/toy_metabolic_input.Rd
man/toy_network.Rd
man/toy_signaling_input.Rd
man/translate_column_HMDB.Rd
man/translate_res.Rd
man/wide_ulm_res.Rd
pkgdown/_pkgdown.yml
pkgdown/extra.css
pkgdown/favicon/apple-touch-icon-120x120.png
pkgdown/favicon/apple-touch-icon-152x152.png
pkgdown/favicon/apple-touch-icon-180x180.png
pkgdown/favicon/apple-touch-icon-60x60.png
pkgdown/favicon/apple-touch-icon-76x76.png
pkgdown/favicon/apple-touch-icon.png
pkgdown/favicon/favicon-16x16.png
pkgdown/favicon/favicon-32x32.png
pkgdown/favicon/favicon.ico
tests/testthat.R
tests/testthat/test-check_COSMOS_inputs.R
tests/testthat/test-cosmos_data.R
tests/testthat/test-load_tf_regulon_dorothea.R
tests/testthat/test-preprocess_COSMOS.R
tests/testthat/test-run_COSMOS_metabolism_to_signaling.R
tests/testthat/test-run_COSMOS_signaling_to_metabolism.R
vignettes/M2Cf/figs/Activity_estimations_for_factor_4_1.png
vignettes/M2Cf/figs/Activity_estimations_for_factor_4_2.png
vignettes/M2Cf/figs/Chekc_cross_correlation_of_omics_compared_to_variance_epxlained_1.png
vignettes/M2Cf/figs/Chekc_cross_correlation_of_omics_compared_to_variance_epxlained_2.png
vignettes/M2Cf/figs/Chekc_cross_correlation_of_omics_compared_to_variance_epxlained_3.png
vignettes/M2Cf/figs/Compare_MOFA_models_1.png
vignettes/M2Cf/figs/Factor_weights_per_view_1.png
vignettes/M2Cf/figs/Plot_Ligand_receptor_activity_estimates_1.png
vignettes/M2Cf/figs/Plot_Metabolite_factor_weights_1.png
vignettes/M2Cf/figs/Plot_RNA_weights_and_protein_weights_1.png
vignettes/M2Cf/figs/Plot_RNA_weights_and_protein_weights_2.png
vignettes/M2Cf/figs/Plot_TF_activity_estimates_1.png
vignettes/M2Cf/figs/Preparing_MOFA_input_1.png
vignettes/M2Cf/figs/Preparing_MOFA_input_2.png
vignettes/M2Cf/figs/Preparing_MOFA_input_3.png
vignettes/M2Cf/figs/Preparing_MOFA_input_4.png
vignettes/M2Cf/figs/Preparing_MOFA_input_5.png
vignettes/M2Cf/figs/Run_moon_rec_to_TFmetab_1.png
vignettes/M2Cf/figs/Supp_figure_condition_prot_RNA_correlation_1.png
vignettes/M2Cf/figs/Supp_figure_single_prot_RNA_correlation_1.png
vignettes/M2Cf/figs/Total_variance_per_factor_1.png
vignettes/M2Cf/figs/Variance_per_view_per_factor_1.png
vignettes/M2Cf/figs/correlation_RNA/prot-1.png
vignettes/M2Cf/figs/run_moon_TF_to_lig_1.png
vignettes/MOFA_to_COSMOS.Rmd
vignettes/MOFA_to_COSMOS.md
vignettes/NCI60_tutorial.Rmd
vignettes/net_compr_MOON.md
vignettes/net_compr_MOON_files/figure-markdown_strict/extract_subnetwork_from_scored_MOON_network_1.png
vignettes/tutorial.Rmd
