notame
This is thereleased version of notame; for the devel version, seenotame.
Workflow for non-targeted LC-MS metabolic profiling
Bioconductor version: Release (3.22)
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]
Maintainer: Vilhelm Suksi <vksuks at utu.fi>
citation("notame")):Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("notame")For older versions of R, please refer to the appropriateBioconductor 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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | BatchEffect,BiomedicalInformatics,DataImport,MassSpectrometry,Metabolomics,MultipleComparison,Normalization,Preprocessing,QualityControl,Software,Visualization |
| Version | 1.0.0 |
| In Bioconductor since | BioC 3.22 (R-4.5) (< 6 months) |
| License | MIT + fileLICENSE |
| 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/notamehttps://hanhineva-lab.github.io/notame/ |
| Bug Reports | https://github.com/hanhineva-lab/notame/issues |
See More
| 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 |
Package Archives
FollowInstallation instructions to use this package in your R session.
| Source Package | notame_1.0.0.tar.gz |
| Windows Binary (x86_64) | notame_1.0.0.zip (64-bit only) |
| macOS Binary (x86_64) | notame_1.0.0.tgz |
| macOS Binary (arm64) | notame_1.0.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/notame |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/notame |
| Bioc Package Browser | https://code.bioconductor.org/browse/notame/ |
| Package Short Url | https://bioconductor.org/packages/notame/ |
| Package Downloads Report | Download Stats |