MetaProViz

This is the development version of MetaProViz; for the stable release version, see MetaProViz.

All versions

METabolomics pre-PRocessing, functiOnal analysis and VIZualisation

Bioconductor version: Development (3.24)

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.

Author: Christina Schmidt [aut, cre, fnd] ORCID: 0000-0002-3867-0881 , Denes Turei [aut] ORCID: 0000-0002-7249-9379 , Dimitrios Prymidis [aut] ORCID: 0009-0000-0168-3841 , Macabe Daley [aut] ORCID: 0000-0002-8026-7068 , Jannik Franken [aut], Julio Saez-Rodriguez [aut] ORCID: 0000-0002-8552-8976 , Christian Frezza [aut] ORCID: 0000-0002-3293-7397

Maintainer: Christina Schmidt <christina.schmidt.science at gmail.com>

Citation (from within R, enter citation("MetaProViz")):

Christina Schmidt, Denes Turei, Dimitrios Prymidis, Macabe Daley, Jannik Franken, Julio Saez-Rodriguez, Christian Frezza. MetaProViz: METabolomics pre-PRocessing, functiOnal analysis and VIZualisation. doi:10.18129/B9.bioc.MetaProViz, R package version 4.1.0, https://bioconductor.org/packages/MetaProViz.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")

BiocManager::install("MetaProViz")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

No vignettes available
Reference Manual	PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Clustering, Metabolomics, Pathways, QualityControl, Software, SystemsBiology, Visualization
Version	4.1.0
In Bioconductor since	BioC 3.23 (R-4.6) (< 6 months)
License	BSD_3_clause + file LICENSE
Depends	R (>= 4.4)
Imports	broom, ComplexUpset (>= 1.3.3), cosmosR, DBI, dplyr, EnhancedVolcano, factoextra, ggbeeswarm, ggfortify, ggplot2 (>= 3.3.5), ggpubr, ggrepel, grid, gridExtra, gtools, hash, igraph, ggraph, inflection, limma, logger, magrittr, methods, OmnipathR (>= 3.19.12), patchwork, pheatmap, Polychrome, purrr, qcc, qvalue, rappdirs, readr, rlang, rstatix, S4Vectors, stringr, SummarizedExperiment, tibble, tidyr, tidyselect, writexl
System Requirements
URL	https://saezlab.github.io/MetaProViz
Bug Reports	https://github.com/saezlab/MetaProViz/issues

Suggests	BiocStyle, ggupset, ggVennDiagram, kableExtra, knitr, pkgdown, svglite, testthat (>= 3.1.4)
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Build Report	Build Report, r-universe

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package
Windows Binary (x86_64)	MetaProViz_4.1.0.zip
macOS Binary (big-sur-x86_64)	MetaProViz_4.1.0.tgz
macOS Binary (sonoma-arm64)	MetaProViz_4.1.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/MetaProViz
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/MetaProViz
Package Short Url	https://bioconductor.org/packages/MetaProViz/
Package Downloads Report	Download Stats