Package: MetaProViz 4.99.0

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], Jannik Franken [aut], Denes Turei [aut], Dimitrios Prymidis [aut], Macabe Daley [aut], Giulia Röth [aut], Julio Saez-Rodriguez [aut], Christian Frezza [aut]

MetaProViz_4.99.0.tar.gz
MetaProViz_4.99.0.zip(r-4.7-any)MetaProViz_4.99.0.zip(r-4.6-any)MetaProViz_4.99.0.zip(r-4.5-any)
MetaProViz_4.99.0.tgz(r-4.6-any)MetaProViz_4.99.0.tgz(r-4.5-any)
MetaProViz_4.99.0.tar.gz(r-4.7-any)MetaProViz_4.99.0.tar.gz(r-4.6-any)
MetaProViz_4.99.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
MetaProViz/json (API)

# 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:

alanine_pathways - Alanine_pathways
biocrates_features - Biocrates_features
cellular_meta - Cellular_meta
equivalent_features - Equivalent_features
gaude_pathways - Gaude_pathways
hallmarks - Hallmarks
intracell_dma - Intracell_dma
intracell_raw - Intracell_raw
intracell_raw_se - Intracell_raw_se
mca_core_rules - Mca_core_rules
mca_twocond_rules - Mca_twocond_rules
medium_raw - Medium_raw
medium_raw_se - Medium_raw_se
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

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

clustering metabolomics pathways qualitycontrol software systemsbiology visualization quarto

7.85 score 26 stars 34 scripts 250 downloads 48 exports 221 dependencies

Last updated from:f76eacf097. Checks:1 NOTE, 7 ERROR, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	275
linux-devel	ERROR	692
source / vignettes	OK	724
linux-release	ERROR	571
macos-release	ERROR	602
macos-oldrel	ERROR	536
windows-devel	ERROR	518
windows-release	ERROR	514
windows-oldrel	ERROR	525
wasm-release	OK	189

Exports:%>%checkmatch_pk_to_data cluster_ora cluster_pk compare_pk core_norm count_id dma equivalent_id feature_filtering get_exclusion_metabolites id_processing make_gene_metab_set mapping_ambiguity mca_2cond mca_core meta_pk metadata_analysis metaproviz_config_path metaproviz_load_config metaproviz_log metaproviz_logfile metaproviz_reset_config metaproviz_save_config metaproviz_set_loglevel metsigdb_chemicalclass metsigdb_kegg metsigdb_macdb metsigdb_metalinks metsigdb_reactome metsigdb_wikipathways mvi_imputation outlier_detection pool_estimation processing replicate_sum seed_id_compatibility_check standard_ora tic_norm translate_id traverse_ids viz_graph viz_heatmap viz_pca viz_pk_network viz_shared_pk_network viz_superplot viz_volcano

Dependencies:abind annotate AnnotationDbi askpass backports base64enc beeswarm BH Biobase BiocBaseUtils BiocGenerics BiocParallel Biostrings bit bit64 blob boot broom bslib cachem car carData CARNIVAL cellranger checkmate cli clipr cluster codetools colorspace ComplexUpset corrplot cosmosR cowplot cpp11 crayon crosstalk curl DBI decoupleR DelayedArray dendextend Deriv digest doBy dplyr DT ellipse emmeans EnhancedVolcano estimability evaluate factoextra FactoMineR farver fastmap flashClust fontawesome forecast formatR Formula fracdiff fs futile.logger futile.options generics GenomicRanges ggbeeswarm ggforce ggfortify ggnewscale ggplot2 ggpubr ggraph ggrepel ggsci ggsignif glue graph graphlayouts gridExtra GSEABase gtable gtools hash highr hms htmltools htmlwidgets httr httr2 igraph inflection IRanges irlba isoband jquerylib jsonlite KEGGREST knitr labeling lambda.r later lattice lazyeval leaps lifecycle limma lme4 lmtest logger lpSolve lubridate magrittr MASS Matrix MatrixGenerics MatrixModels matrixStats memoise mgcv mime minqa modelr multcompView mvtnorm nlme nloptr nnet numDeriv OmnipathR openssl otel parallelly patchwork pbkrtest pheatmap pillar pkgconfig plyr png Polychrome polyclip polynom prettyunits progress promises purrr quantreg qvalue R.methodsS3 R.oo R.utils R6 rappdirs rbibutils RColorBrewer Rcpp RcppArmadillo RcppEigen Rdpack readr readxl reformulas rematch reshape2 rjson rlang rmarkdown RSQLite rstatix rvest S4Arrays S4Vectors S7 sass scales scatterplot3d selectr Seqinfo sessioninfo showtext showtextdb snow SparseArray SparseM statmod stringi stringr SummarizedExperiment survival sys sysfonts systemfonts tibble tidygraph tidyr tidyselect timechange timeDate tinytex tweenr tzdb urca utf8 vctrs vipor viridis viridisLite visNetwork vroom withr writexl xfun XML xml2 xtable XVector yaml zip zoo

Getting started with MetaProViz

Rendered fromquick-start.Rmdusingknitr::rmarkdown

Last update: 2026-10-02
Started: 2025-10-07

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

Package: MetaProViz 4.99.0

MetaProViz: METabolomics pre-PRocessing, functiOnal analysis and VIZualisation

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Help Manual

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