notameViz

Workflow for non-targeted LC-MS metabolic profiling

Bioconductor version: 3.23 · Package version: 1.2.0

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

Installation

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

BiocManager::install("notameViz")

Details

Maintainer	Vilhelm Suksi <vksuks@utu.fi>
Author	Anton Klåvus [aut, cph] (ORCID: <https://orcid.org/0000-0003-2612-0230>), Jussi Paananen [aut, cph] (ORCID: <https://orcid.org/0000-0001-5100-4907>), Oskari Timonen [aut, cph] (ORCID: <https://orcid.org/0000-0002-6317-6260>), Atte Lihtamo [aut], Vilhelm Suksi [aut, cre] (ORCID: <https://orcid.org/0009-0005-1108-518X>), Retu Haikonen [aut] (ORCID: <https://orcid.org/0000-0003-0830-3850>), Leo Lahti [aut] (ORCID: <https://orcid.org/0000-0001-5537-637X>), Kati Hanhineva [aut] (ORCID: <https://orcid.org/0000-0001-6834-7375>), Ville Koistinen [ctb] (ORCID: <https://orcid.org/0000-0003-1587-8361>), Olli Kärkkäinen [ctb] (ORCID: <https://orcid.org/0000-0003-0825-4956>), Artur Sannikov [ctb]
License	MIT + file LICENSE
URL	https://github.com/hanhineva-lab/notameViz
Bug Reports	https://github.com/hanhineva-lab/notameViz/issues
Downloads rank	131
Source branch	RELEASE_3_23
biocViews	BatchEffect, BiomedicalInformatics, DataImport, MassSpectrometry, Metabolomics, MultipleComparison, Normalization, Preprocessing, QualityControl, Software, Visualization

Documentation

Non-targeted metabolomics visualization

Download

Source package

Dependencies

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

Suggests: batchCorr, BiocStyle, igraph, knitr, notameStats, testthat

Reverse dependencies

Suggests Me (2): notame, notameStats