notame

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

All versions

Workflow for non-targeted LC-MS metabolic profiling

Bioconductor version: Release (3.23)

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] ORCID: 0000-0003-2612-0230 , Jussi Paananen [aut, cph] ORCID: 0000-0001-5100-4907 , Oskari Timonen [aut, cph] ORCID: 0000-0002-6317-6260 , Atte Lihtamo [aut], Vilhelm Suksi [aut, cre] ORCID: 0009-0005-1108-518X , Retu Haikonen [aut] ORCID: 0000-0003-0830-3850 , Leo Lahti [aut] ORCID: 0000-0001-5537-637X , Kati Hanhineva [aut] ORCID: 0000-0001-6834-7375 , Ville Koistinen [ctb] ORCID: 0000-0003-1587-8361 , Olli Kärkkäinen [ctb] ORCID: 0000-0003-0825-4956 , Artur Sannikov [ctb] ORCID: 0000-0001-7765-123X

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 1.2.0, 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")

BiocManager::install("notame")

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("notame")

Non-targeted metabolomics preprocessing and wrangling	HTML	R Script
Project example	HTML	R Script
Reference Manual	PDF
NEWS	Text
LICENSE	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	BatchEffect, BiomedicalInformatics, DataImport, MassSpectrometry, Metabolomics, MultipleComparison, Normalization, Preprocessing, QualityControl, Software, Visualization
Version	1.2.0
In Bioconductor since	BioC 3.22 (R-4.5) (1 year)
License	MIT + file LICENSE
Depends	R (>= 4.5.0), ggplot2, SummarizedExperiment
Imports	BiocGenerics, BiocParallel, dplyr, futile.logger, methods, openxlsx, S4Vectors, scales, stringr, tidyr, utils
System Requirements
URL	https://github.com/hanhineva-lab/notame https://hanhineva-lab.github.io/notame/
Bug Reports	https://github.com/hanhineva-lab/notame/issues

Suggests	BiocStyle, fpc, igraph, knitr, missForest, notameViz, notameStats, pcaMethods, RUVSeq, testthat
Linking To
Enhances
Depends On Me
Imports Me	notameStats, notameViz
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	notame_1.2.0.tar.gz
Windows Binary (x86_64)	notame_1.2.0.zip
macOS Binary (big-sur-x86_64)	notame_1.2.0.tgz
macOS Binary (sonoma-arm64)	notame_1.2.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/notame
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/notame
Package Short Url	https://bioconductor.org/packages/notame/
Package Downloads Report	Download Stats