Package: MetaProViz 4.1.0

Christina Schmidt

MetaProViz: METabolomics pre-PRocessing, functiOnal analysis and VIZualisation

MetaProViz can analyse standard metabolomics and exometabolomics data (CoRe). It performs pre-processing including feature filtering, missing value imputation, normalisation and outlier detection. It performs functional analysis including differential metabolite analysis (DMA), clustering based on regulatory rules (MCA) and contains different visualisation methods to extract biological interpretable graphs and saves them in a publication ready format.

Authors:Christina Schmidt [aut, cre, fnd], Denes Turei [aut], Dimitrios Prymidis [aut], Macabe Daley [aut], Jannik Franken [aut], Julio Saez-Rodriguez [aut], Christian Frezza [aut]

MetaProViz_4.1.0.tar.gz
MetaProViz_4.1.0.zip(r-4.7)MetaProViz_4.1.0.zip(r-4.6)MetaProViz_4.1.0.zip(r-4.5)
MetaProViz_4.1.0.tgz(r-4.6-any)MetaProViz_4.1.0.tgz(r-4.5-any)
MetaProViz_4.1.0.tar.gz(r-4.7-any)MetaProViz_4.1.0.tar.gz(r-4.6-any)
MetaProViz_4.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
MetaProViz/json (API)
NEWS

# Install 'MetaProViz' in R:
install.packages('MetaProViz', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/saezlab/metaproviz/issues

Pkgdown/docs site:https://saezlab.github.io

Datasets:

On BioConductor:MetaProViz-4.1.0(bioc 3.24)MetaProViz-4.0.0(bioc 3.23)

clusteringmetabolomicspathwaysqualitycontrolsoftwaresystemsbiologyvisualizationquarto

7.44 score 20 stars 30 scripts 219 downloads 39 exports 218 dependencies

Last updated from:02799d0d5a. Checks:1 ERROR, 4 NOTE, 2 OK, 3 WARNING. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksERROR269
linux-devel-x86_64NOTE760
source / vignettesOK524
linux-release-x86_64NOTE711
macos-release-arm64NOTE555
macos-oldrel-arm64NOTE634
windows-develWARNING889
windows-releaseWARNING778
windows-oldrelWARNING918
wasm-releaseOK243

Exports:%>%checkmatch_pk_to_datacluster_oracluster_pkcompare_pkcount_iddmaequivalent_idget_exclusion_metabolitesmake_gene_metab_setmapping_ambiguitymca_2condmca_coremeta_pkmetadata_analysismetaproviz_config_pathmetaproviz_load_configmetaproviz_logmetaproviz_logfilemetaproviz_reset_configmetaproviz_save_configmetaproviz_set_loglevelmetsigdb_chemicalclassmetsigdb_keggmetsigdb_macdbmetsigdb_metalinksmetsigdb_reactomemetsigdb_wikipathwayspool_estimationprocessingreplicate_sumstandard_oratranslate_idtraverse_idsviz_graphviz_heatmapviz_pcaviz_superplotviz_volcano

Dependencies:abindannotateAnnotationDbiaskpassbackportsbase64encbeeswarmBHBiobaseBiocGenericsBiocParallelBiostringsbitbit64blobbootbroombslibcachemcarcarDataCARNIVALcellrangercheckmateclicliprclustercodetoolscolorspaceComplexUpsetcorrplotcosmosRcowplotcpp11crayoncrosstalkcurlDBIdecoupleRDelayedArraydendextendDerivdigestdoBydorotheadplyrDTellipseemmeansEnhancedVolcanoestimabilityevaluatefactoextraFactoMineRfarverfastmapflashClustfontawesomeforecastformatRFormulafracdifffsfutile.loggerfutile.optionsgenericsGenomicRangesggbeeswarmggforceggfortifyggplot2ggpubrggraphggrepelggsciggsignifgluegraphgraphlayoutsgridExtraGSEABasegtablegtoolshashhighrhmshtmltoolshtmlwidgetshttrhttr2igraphinflectionIRangesisobandjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlaterlatticelazyevalleapslifecyclelimmalme4lmtestloggerlpSolvelubridatemagrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmemoisemgcvmicrobenchmarkmimeminqamodelrmultcompViewmvtnormnlmenloptrnnetnumDerivOmnipathRopensslotelparallellypatchworkpbkrtestpheatmappillarpkgconfigplyrpngPolychromepolyclippolynomprettyunitsprogresspromisespurrrqccquantregqvalueR.methodsS3R.ooR.utilsR6rappdirsrbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRdpackreadrreadxlreformulasrematchreshape2rjsonrlangrmarkdownRSQLiterstatixrvestS4ArraysS4VectorsS7sassscalesscatterplot3dselectrSeqinfosessioninfosnowSparseArraySparseMstatmodstringistringrSummarizedExperimentsurvivalsyssystemfontstibbletidygraphtidyrtidyselecttimechangetimeDatetinytextweenrtzdburcautf8vctrsviporviridisviridisLitevisNetworkvroomwithrwritexlxfunXMLxml2xtableXVectoryamlzipzoo

Getting started with MetaProViz

Christina Schmidt

Rendered fromquick-start.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2026-03-23
Started: 2025-10-07

Readme and manuals

Help Manual

Help pageTopics
alanine_pathwaysalanine_pathways
biocrates_featuresbiocrates_features
cellular_metacellular_meta
Check and summarize relationship between prixor knowledge to measuredcheckmatch_pk_to_data
Overrepresentation analysis by clustercluster_ora
Cluster terms in prior knowledge by set overlapcluster_pk
Compare Prior Knowledge Resources and/or Columns within a Single Resourcecompare_pk
Count Entries and Generate a Histogram Plot for a Specified Columncount_id
Differential metabolite analysisdma
equivalent_featuresequivalent_features
Find additional potential IDs for "kegg", "pubchem", "chebi", "hmdb"equivalent_id
gaude_pathwaysgaude_pathways
Metabolites excluded from prior knowledge resourcesget_exclusion_metabolites
hallmarkshallmarks
intracell_dmaintracell_dma
intracell_rawintracell_raw
intracell_raw_seintracell_raw_se
Create metabolite sets from existing genesetsmake_gene_metab_set
Create Mapping Ambiguities between two ID typesmapping_ambiguity
Metabolite clustering analysis for two conditionsmca_2cond
Metabolite clustering analysis for core experimentsmca_core
mca_core_rulesmca_core_rules
mca_twocond_rulesmca_twocond_rules
medium_rawmedium_raw
Meta prior-knowledgemeta_pk
PCA-based metadata analysismetadata_analysis
The MetaProViz packageMetaProViz-package MetaProViz
Current config file path of MetaProVizmetaproviz_config_path
Load the package configuration from a config filemetaproviz_load_config
Browse the current MetaProViz log filemetaproviz_log
Path to the current MetaProViz log filemetaproviz_logfile
Restore the built-in default values of all config parameters of MetaProVizmetaproviz_reset_config
Save the current package configurationmetaproviz_save_config
Sets the log level for the package loggermetaproviz_set_loglevel
Metabolite chemical classes from RaMP DBmetsigdb_chemicalclass
KEGG pathwaysmetsigdb_kegg
Retrieve MACDB metabolite-cancer associations.metsigdb_macdb
Annotated metabolite-protein interactions from MetalinksDBmetsigdb_metalinks
Retrieve Reactome metabolite sets suitable for ORA.metsigdb_reactome
Retrieve WikiPathways metabolite mapping suitable for ORA.metsigdb_wikipathways
Find metabolites with high variability across total pool samplespool_estimation
Data preprocessing and normalizationprocessing
Merges the analytical replicates of an experimentreplicate_sum
Overrepresentation analysis of metabolite sets in pathwaysstandard_ora
tissue_dmatissue_dma
tissue_dma_oldtissue_dma_old
tissue_dma_youngtissue_dma_young
Tissue_Metadatatissue_meta
tissue_normtissue_norm
tissue_norm_setissue_norm_se
tissue_tvn_proteomicstissue_tvn_proteomics
tissue_tvn_rnaseqtissue_tvn_rnaseq
Translate IDs to/from KEGG, PubChem, Chebi, HMDBtranslate_id
Expand metabolite IDs by traversing RaMP ID mappingstraverse_ids
Graph visualization for clustered termsviz_graph
Heatmap visualizationviz_heatmap
This script allows you to perform PCA plot visualization using the results of the MetaProViz analysisviz_pca
This script allows you to perform different visualizations (bar, box, violin plots) using the results of the MetaProViz analysisviz_superplot
Volcano plotviz_volcano