notame
This is the development version of notame; for the stable release version, see notame.
All Bioconductor versions of notame
3.24 (devel), 3.23 (release), 3.22
Workflow for non-targeted LC-MS metabolic profiling
Bioconductor version: 3.24 · Package version: 1.3.0
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.
Author: Anton Klåvus [aut, cph] 
, Jussi Paananen [aut, cph] , Oskari Timonen [aut, cph] , Atte Lihtamo [aut], Vilhelm Suksi [aut, cre] , Retu Haikonen [aut] , Leo Lahti [aut] , Kati Hanhineva [aut] , Ville Koistinen [ctb] , Olli Kärkkäinen [ctb] , Artur Sannikov [ctb]
Maintainer: Vilhelm Suksi <vksuks at utu.fi>
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.
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("notame")For older versions of R, please refer to the appropriate Bioconductor release.
Details
| Version | 1.3.0 |
| 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 |
| Last updated | 2026-04-28 |
| In Bioconductor since | BioC 3.22 (R-4.5) (less than a year) |
| Downloads rank | 2092 of 2,456 |
| 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/ |
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("notame")| Non-targeted metabolomics preprocessing and data wrangling | HTML | R Script |
| Project example | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
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 |
| Source Repository | git clone https://git.bioconductor.org/packages/notame |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/notame |
| Package Downloads Report | Download Stats |
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