Files in borenstein-lab/mimosa2

Model-based Integration of Metabolite Observations and Species Abundances

R/RcppExports.R R/core_functions.R R/core_mimosa2_funcs.R R/misc_helper_functions.R R/postProcessing.R R/shuffle_network.R R/singleSpec_contributions.R R/speciesPicrustFunctions.R R/taxa_agora.R README.md man/add_metadata_to_metabolite_summary.Rd man/add_residuals.Rd man/add_rev_rxns.Rd man/add_to_network.Rd man/agora_kegg_mets.Rd man/basic_correlation_matrix.Rd man/blast_seqs.Rd man/build_generic_network.Rd man/build_metabolic_model.Rd man/build_species_networks_w_agora.Rd man/calculate_var_shares.Rd man/calculate_var_shares_linear.Rd man/check_config_table.Rd man/check_ref_data.Rd man/cmp_met_plot.Rd man/cmp_species_contributions.Rd man/cmp_species_contributions_picrust.Rd man/compare_met.Rd man/contribs_by_species_list.Rd man/correct.Rd man/download_reference_data.Rd man/download_ribosomal_ref_seqs.Rd man/emm_to_edge_list.Rd man/filter_currency_metabolites.Rd man/filter_species_abunds.Rd man/fit_cmp_mods.Rd man/fit_cmp_net_edit.Rd man/fit_single_scaling_mod.Rd man/g_legend.Rd man/gene_contributions.Rd man/generate_contribution_table_using_picrust.Rd man/generate_genomic_network.Rd man/generate_network_template_kegg.Rd man/generate_preprocessed_networks.Rd man/getModelInfo.Rd man/getWScores.Rd man/get_S_mats.Rd man/get_all_consistent_metabolite_info.Rd man/get_all_singleSpec_cmps.Rd man/get_analysis_summary.Rd man/get_cmp_scores.Rd man/get_cmp_scores_kos.Rd man/get_cmp_summary.Rd man/get_compound_format.Rd man/get_genomic_content_from_picrust_table.Rd man/get_kegg_network.Rd man/get_kegg_reaction_info.Rd man/get_net_dist.Rd man/get_non_rev_rxns.Rd man/get_rep_seqs_from_otus.Rd man/get_spec_contribs.Rd man/get_species_cmp_scores.Rd man/get_subset_picrust_ko_table.Rd man/get_summary_stats.Rd man/get_text.Rd man/humann2_format_contributions.Rd man/img_uri.Rd man/j.disp.fit.Rd man/j.disp.mean.Rd man/j.disp.rsq.adj.Rd man/kegg_agora_mets.Rd man/kos_from_species.Rd man/load_agora_models.Rd man/make_contrib_network.Rd man/make_gene_species_contributor_table.Rd man/make_metabolite_species_contribution_table.Rd man/make_network_matrix.Rd man/make_pairwise_met_matrix.Rd man/make_perm_mat.Rd man/make_unnormalized_single_spec.Rd man/mantel_2sided.Rd man/map_seqvar.Rd man/map_to_kegg_webchem.Rd man/met_names.Rd man/met_table_fix.Rd man/otus_to_db.Rd man/plot_all_cmp_mets.Rd man/plot_contrib_net.Rd man/plot_contributions.Rd man/plot_metabolite_concentrations.Rd man/plot_metabolite_counts.Rd man/plot_summary_contributions.Rd man/print_taxa_contributor_table.Rd man/process_gene_contribs.Rd man/process_mat_met_file.Rd man/process_metabolite_summary.Rd man/randomString.Rd man/randomize_net.Rd man/rank_based_rsq_contribs.Rd man/read_files.Rd man/read_mimosa2_files.Rd man/refine_rev_rxns.Rd man/run_all_metabolites.Rd man/run_all_metabolites2.Rd man/run_all_metabolites_FBA2.Rd man/run_mimosa1.Rd man/run_mimosa2.Rd man/run_samp_shapley_analysis.Rd man/run_shapley_contrib_analysis.Rd man/run_shuffle.Rd man/single_gene_cmp.Rd man/single_spec_musicc.Rd man/spec_table_fix.Rd man/sum_to_genus.Rd man/taxonomic_contributor_heatmap_plot_grid.Rd man/test_m2_analysis.Rd man/test_met_enrichment.Rd man/transform_cmps.Rd man/transform_mets.Rd man/var_shares_cmps.Rd tests/testthat.R tests/testthat/test_core.R tests/testthat/test_mimosa2.R