notame
Workflow for non-targeted LC-MS metabolic profiling
Bioconductor version: 3.24 · Package version: 1.3.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
Provides functionality for untargeted LC-MS metabolomics research as specified in the associated protocol article in the 'Metabolomics Data Processing and Data Analysis—Current Best Practices' special issue of the Metabolites journal (2020). This includes tabular data preprocessing and quality control, uni- and multivariate analysis as well as quality control visualizations, feature-wise visualizations and results visualizations. Raw data preprocessing and functionality related to biological context, such as pathway analysis, is not included.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("notame")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] (ORCID: <https://orcid.org/0000-0001-7765-123X>) |
| License | MIT + file LICENSE |
| URL | https://github.com/hanhineva-lab/notame, https://hanhineva-lab.github.io/notame/ |
| Bug Reports | https://github.com/hanhineva-lab/notame/issues |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | BatchEffect, BiomedicalInformatics, DataImport, MassSpectrometry, Metabolomics, MultipleComparison, Normalization, Preprocessing, QualityControl, Software, Visualization |
| Package Short Url | https://bioconductor.org/packages/notame/ |
Citation
From within R, enter citation("notame"):
Anton Klåvus, Jussi Paananen, Oskari Timonen, Atte Lihtamo, Vilhelm Suksi, Retu Haikonen, Leo Lahti, Kati Hanhineva. notame: Workflow for non-targeted LC-MS metabolic profiling. doi:10.18129/B9.bioc.notame, R package version 1.3.0, https://bioconductor.org/packages/notame.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | notame_1.3.0.tar.gz |
| Windows binary (x86_64) | notame_1.3.0.zip |
| macOS binary (arm64) | notame_1.3.0.tgz |
| macOS binary (x86_64) | notame_1.3.0.tgz |
Dependencies
Depends: R (>= 4.5.0), ggplot2, SummarizedExperiment
Imports: BiocGenerics, BiocParallel, dplyr, futile.logger, methods, openxlsx, S4Vectors, scales, stringr, tidyr, utils
Suggests: BiocStyle, fpc, igraph, knitr, missForest, notameViz, notameStats, pcaMethods, RUVSeq, testthat
Reverse dependencies
Imports Me (2): notameStats, notameViz