METabolomics pre-PRocessing, functiOnal analysis and
VIZualisation
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Documentation for package ‘MetaProViz’ version 3.99.50
Help Pages
| MetaProViz-package | The MetaProViz package |
| alanine_pathways | alanine_pathways |
| biocrates_features | biocrates_features |
| cellular_meta | cellular_meta |
| checkmatch_pk_to_data | Check and summarize relationship between prixor knowledge to measured |
| cluster_ora | Overrepresentation analysis by cluster |
| cluster_pk | Cluster terms in prior knowledge by set overlap |
| compare_pk | Compare Prior Knowledge Resources and/or Columns within a Single Resource |
| count_id | Count Entries and Generate a Histogram Plot for a Specified Column |
| dma | Differential metabolite analysis |
| equivalent_features | equivalent_features |
| equivalent_id | Find additional potential IDs for "kegg", "pubchem", "chebi", "hmdb" |
| gaude_pathways | gaude_pathways |
| get_exclusion_metabolites | Metabolites excluded from prior knowledge resources |
| hallmarks | hallmarks |
| intracell_dma | intracell_dma |
| intracell_raw | intracell_raw |
| intracell_raw_se | intracell_raw_se |
| make_gene_metab_set | Create metabolite sets from existing genesets |
| mapping_ambiguity | Create Mapping Ambiguities between two ID types |
| mca_2cond | Metabolite clustering analysis for two conditions |
| mca_core | Metabolite clustering analysis for core experiments |
| mca_core_rules | mca_core_rules |
| mca_twocond_rules | mca_twocond_rules |
| medium_raw | medium_raw |
| metadata_analysis | PCA-based metadata analysis |
| MetaProViz | The MetaProViz package |
| metaproviz_config_path | Current config file path of MetaProViz |
| metaproviz_load_config | Load the package configuration from a config file |
| metaproviz_log | Browse the current MetaProViz log file |
| metaproviz_logfile | Path to the current MetaProViz log file |
| metaproviz_reset_config | Restore the built-in default values of all config parameters of MetaProViz |
| metaproviz_save_config | Save the current package configuration |
| metaproviz_set_loglevel | Sets the log level for the package logger |
| meta_pk | Meta prior-knowledge |
| metsigdb_chemicalclass | Metabolite chemical classes from RaMP DB |
| metsigdb_kegg | KEGG pathways |
| metsigdb_macdb | Retrieve MACDB metabolite-cancer associations. |
| metsigdb_metalinks | Annotated metabolite-protein interactions from MetalinksDB |
| metsigdb_reactome | Retrieve Reactome metabolite sets suitable for ORA. |
| metsigdb_wikipathways | Retrieve WikiPathways metabolite mapping suitable for ORA. |
| pool_estimation | Find metabolites with high variability across total pool samples |
| processing | Data preprocessing and normalization |
| replicate_sum | Merges the analytical replicates of an experiment |
| standard_ora | Overrepresentation analysis of metabolite sets in pathways |
| tissue_dma | tissue_dma |
| tissue_dma_old | tissue_dma_old |
| tissue_dma_young | tissue_dma_young |
| tissue_meta | Tissue_Metadata |
| tissue_norm | tissue_norm |
| tissue_norm_se | tissue_norm_se |
| tissue_tvn_proteomics | tissue_tvn_proteomics |
| tissue_tvn_rnaseq | tissue_tvn_rnaseq |
| translate_id | Translate IDs to/from KEGG, PubChem, Chebi, HMDB |
| traverse_ids | Expand metabolite IDs by traversing RaMP ID mappings |
| viz_graph | Graph visualization for clustered terms |
| viz_heatmap | Heatmap visualization |
| viz_pca | This script allows you to perform PCA plot visualization using the results of the MetaProViz analysis |
| viz_superplot | This script allows you to perform different visualizations (bar, box, violin plots) using the results of the MetaProViz analysis |
| viz_volcano | Volcano plot |