MetaProViz
This is the released version of MetaProViz; for the devel version, see MetaProViz.
METabolomics pre-PRocessing, functiOnal analysis and VIZualisation
Bioconductor version: Release (3.23)
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] 
, Denes Turei [aut] , Dimitrios Prymidis [aut] , Macabe Daley [aut] , Jannik Franken [aut], Julio Saez-Rodriguez [aut] , Christian Frezza [aut]
Maintainer: Christina Schmidt <christina.schmidt.science at gmail.com>
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 4.0.0, 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")
BiocManager::install("MetaProViz")For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("MetaProViz")| Quick Overview | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Clustering, Metabolomics, Pathways, QualityControl, Software, SystemsBiology, Visualization |
| Version | 4.0.0 |
| 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 |
See More
| Suggests | BiocStyle, ggupset, ggVennDiagram, kableExtra, knitr, pkgdown, svglite, testthat (>= 3.1.4) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | MetaProViz_4.0.0.tar.gz |
| Windows Binary (x86_64) | MetaProViz_4.0.0.zip |
| macOS Binary (big-sur-x86_64) | MetaProViz_4.0.0.tgz |
| macOS Binary (sonoma-arm64) | MetaProViz_4.0.0.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 |