API for borenstein-lab/mimosa2
Model-based Integration of Metabolite Observations and Species Abundances
| Global functions | |
|---|---|
| add_metadata_to_metabolite_summary | Man page Source code |
| add_residuals | Man page Source code |
| add_rev_rxns | Man page Source code |
| add_to_network | Man page Source code |
| agora_kegg_mets | Man page Source code |
| basic_correlation_matrix | Man page Source code |
| blast_seqs | Man page Source code |
| build_generic_network | Man page Source code |
| build_metabolic_model | Man page Source code |
| build_model_components | Source code |
| build_species_networks_w_agora | Man page Source code |
| calculate_var_shares | Man page Source code |
| calculate_var_shares_linear | Man page Source code |
| check_config_table | Man page Source code |
| check_ref_data | Man page Source code |
| cmp_met_plot | Man page Source code |
| cmp_species_contributions | Man page Source code |
| cmp_species_contributions_picrust | Man page Source code |
| compare_met | Man page Source code |
| contribs_by_species_list | Man page Source code |
| correct | Man page Source code |
| download_reference_data | Man page Source code |
| download_ribosomal_ref_seqs | Man page Source code |
| emm_to_edge_list | Man page Source code |
| filter_currency_metabolites | Man page Source code |
| filter_species_abunds | Man page Source code |
| fit_cmp_mods | Man page Source code |
| fit_cmp_net_edit | Man page Source code |
| fit_single_scaling_mod | Man page Source code |
| g_legend | Man page Source code |
| gene_contributions | Man page Source code |
| generate_contribution_table_using_picrust | Man page Source code |
| generate_genomic_network | Man page Source code |
| generate_network_template_kegg | Man page Source code |
| generate_preprocessed_networks | Man page Source code |
| getModelInfo | Man page Source code |
| getWScores | Man page Source code |
| get_S_mats | Man page Source code |
| get_all_consistent_metabolite_info | Man page Source code |
| get_all_singleSpec_cmps | Man page Source code |
| get_analysis_summary | Man page Source code |
| get_cmp_scores | Man page Source code |
| get_cmp_scores_kos | Man page Source code |
| get_cmp_summary | Man page Source code |
| get_compound_format | Man page Source code |
| get_genomic_content_from_picrust_table | Man page Source code |
| get_kegg_network | Man page Source code |
| get_kegg_reaction_info | Man page Source code |
| get_kegg_reaction_links | Source code |
| get_net_dist | Man page Source code |
| get_non_rev_rxns | Man page Source code |
| get_rep_seqs_from_otus | Man page Source code |
| get_spec_contribs | Man page Source code |
| get_species_cmp_scores | Man page Source code |
| get_subset_picrust_ko_table | Man page Source code |
| get_summary_stats | Man page Source code |
| get_text | Man page Source code |
| ggMMplot | Source code |
| humann2_format_contributions | Man page Source code |
| img_uri | Man page Source code |
| j.disp.fit | Man page Source code |
| j.disp.mean | Man page Source code |
| j.disp.rsq.adj | Man page Source code |
| kegg_agora_mets | Man page Source code |
| kos_from_species | Man page Source code |
| load_agora_models | Man page Source code |
| make_contrib_network | Man page Source code |
| make_gene_species_contributor_table | Man page Source code |
| make_metabolite_species_contribution_table | Man page Source code |
| make_network_matrix | Man page Source code Source code |
| make_pairwise_met_matrix | Man page Source code |
| make_perm_mat | Man page Source code |
| make_unnormalized_single_spec | Man page Source code |
| mantel_2sided | Man page |
| map_hmdb_to_kegg_webchem | Source code |
| map_seqvar | Man page Source code |
| map_to_kegg_webchem | Man page Source code |
| met_names | Man page Source code |
| met_table_fix | Man page Source code |
| otus_to_db | Man page Source code |
| plot_all_cmp_mets | Man page Source code |
| plot_contrib_net | Man page Source code |
| plot_contributions | Man page Source code |
| plot_mantel_results | Source code |
| plot_metabolite_concentrations | Man page Source code |
| plot_metabolite_counts | Man page Source code |
| plot_ref_mets_by_cmps | Source code |
| plot_summary_contributions | Man page Source code |
| print_taxa_contributor_table | Man page Source code |
| process_gene_contribs | Man page Source code |
| process_mat_met_file | Man page Source code |
| process_metabolite_summary | Man page Source code |
| randomShuffle | Source code |
| randomString | Man page Source code |
| randomize_net | Man page Source code Source code |
| rank_based_rsq_contribs | Man page Source code |
| read_files | Man page Source code |
| read_mimosa2_files | Man page Source code |
| refine_rev_rxns | Man page Source code |
| run_all_metabolites | Man page Source code |
| run_all_metabolites2 | Man page Source code |
| run_all_metabolites_FBA2 | Man page Source code |
| run_mimosa1 | Man page Source code |
| run_mimosa2 | Man page Source code |
| run_samp_shapley_analysis | Man page Source code |
| run_shapley_contrib_analysis | Man page Source code |
| run_shuffle | Man page Source code |
| select_best_id | Source code |
| select_best_id2 | Source code |
| simpleCap | Source code |
| single_gene_cmp | Man page Source code |
| single_spec_musicc | Man page Source code |
| spec_table_fix | Man page Source code |
| sum_to_genus | Man page Source code |
| taxonomic_contributor_heatmap_plot_grid | Man page Source code |
| test_m2_analysis | Man page Source code |
| test_met_enrichment | Man page Source code |
| transform_cmps | Man page Source code |
| transform_mets | Man page Source code |
| var_shares_cmps | Man page Source code |
