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notameViz

This is the released version of notameViz; for the devel version, see notameViz.

All versions 3.24 (devel), 3.23 (release), 3.22

Workflow for non-targeted LC-MS metabolic profiling


Bioconductor version: Release (3.23)

Provides visualization functionality for untargeted LC-MS metabolomics research. Includes quality control visualizations, feature-wise visualizations and results visualizations.

Author: Anton Klåvus [aut, cph] ORCID iD ORCID: 0000-0003-2612-0230 , Jussi Paananen [aut, cph] ORCID iD ORCID: 0000-0001-5100-4907 , Oskari Timonen [aut, cph] ORCID iD ORCID: 0000-0002-6317-6260 , Atte Lihtamo [aut], Vilhelm Suksi [aut, cre] ORCID iD ORCID: 0009-0005-1108-518X , Retu Haikonen [aut] ORCID iD ORCID: 0000-0003-0830-3850 , Leo Lahti [aut] ORCID iD ORCID: 0000-0001-5537-637X , Kati Hanhineva [aut] ORCID iD ORCID: 0000-0001-6834-7375 , Ville Koistinen [ctb] ORCID iD ORCID: 0000-0003-1587-8361 , Olli Kärkkäinen [ctb] ORCID iD ORCID: 0000-0003-0825-4956 , Artur Sannikov [ctb]

Maintainer: Vilhelm Suksi <vksuks at utu.fi>

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

Anton Klåvus, Jussi Paananen, Oskari Timonen, Atte Lihtamo, Vilhelm Suksi, Retu Haikonen, Leo Lahti, Kati Hanhineva. notameViz: Workflow for non-targeted LC-MS metabolic profiling. doi:10.18129/B9.bioc.notameViz, R package version 1.2.0, https://bioconductor.org/packages/notameViz.

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("notameViz")

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("notameViz")
Non-targeted metabolomics visualization HTML R Script
Reference ManualPDF
NEWSText
LICENSEText
Need some help? Ask on the Bioconductor Support site!

Details

biocViews BatchEffect, BiomedicalInformatics, DataImport, MassSpectrometry, Metabolomics, MultipleComparison, Normalization, Preprocessing, QualityControl, Software, Visualization
Version1.2.0
In Bioconductor sinceBioC 3.22 (R-4.5) (1 year)
License MIT + file LICENSE
Depends R (>= 4.5.0), ggplot2, SummarizedExperiment
Imports BiocGenerics, cowplot, devEMF, dplyr, ggbeeswarm, ggdendro, ggrepel, grDevices, limma, methods, notame, pcaMethods, qpdf, Rtsne, scales, stringr, stats, tibble, tidyr, utils
System Requirements
URLhttps://github.com/hanhineva-lab/notameViz
Bug Reportshttps://github.com/hanhineva-lab/notameViz/issues
See More
Suggests batchCorr, BiocStyle, igraph, knitr, notameStats, testthat
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me notame, notameStats
Links To Me
Build Report Build Report, r-universe

Package Archives

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

Source Package notameViz_1.2.0.tar.gz
Windows Binary (x86_64) notameViz_1.2.0.zip
macOS Binary (big-sur-x86_64) notameViz_1.2.0.tgz
macOS Binary (sonoma-arm64) notameViz_1.2.0.tgz
Source Repositorygit clone https://git.bioconductor.org/packages/notameViz
Source Repository (Developer Access)git clone git@git.bioconductor.org:packages/notameViz
Package Short Url https://bioconductor.org/packages/notameViz/
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