Package index • MetaProViz

All functions

MetaProViz-package MetaProViz: 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
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
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
meta_pk(): Meta prior-knowledge
metadata_analysis(): PCA-based metadata analysis
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
metsigdb_chemicalclass(): Metabolite chemical classes from RaMP DB
metsigdb_kegg(): KEGG pathways
metsigdb_metalinks(): Annotated metabolite-protein interactions from MetalinksDB
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
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