lipidr

DOI: 10.18129/B9.bioc.lipidr    

This is the development version of lipidr; for the stable release version, see lipidr.

Data Mining and Analysis of Lipidomics Datasets

Bioconductor version: Development (3.11)

lipidr an easy-to-use R package implementing a complete workflow for downstream analysis of targeted and untargeted lipidomics data. lipidomics results can be imported into lipidr as a numerical matrix or a Skyline export, allowing integration into current analysis frameworks. Data mining of lipidomics datasets is enabled through integration with Metabolomics Workbench API. lipidr allows data inspection, normalization, univariate and multivariate analysis, displaying informative visualizations. lipidr also implements a novel Lipid Set Enrichment Analysis (LSEA), harnessing molecular information such as lipid class, chain length and unsaturation.

Author: Ahmed Mohamed [cre] , Ahmed Mohamed [aut], Jeffrey Molendijk [aut]

Maintainer: Ahmed Mohamed <mohamed at kuicr.kyoto-u.ac.jp>

Citation (from within R, enter citation("lipidr")):

Installation

To install this package, start R (version "4.0") and enter:

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("lipidr")

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("lipidr")

 

HTML R Script lipidr_workflow
PDF   Reference Manual
Text   NEWS
Text   LICENSE

Details

biocViews Lipidomics, MassSpectrometry, Normalization, QualityControl, Software, Visualization
Version 2.1.2
In Bioconductor since BioC 3.9 (R-3.6) (0.5 years)
License MIT + file LICENSE
Depends R (>= 3.6.0), SummarizedExperiment
Imports methods, stats, utils, data.table, S4Vectors, rlang, dplyr, tidyr, forcats, ggplot2, limma, fgsea, ropls, magrittr
LinkingTo
Suggests knitr, rmarkdown, BiocStyle, ggrepel, plotly, iheatmapr, spelling, testthat
SystemRequirements
Enhances
URL https://github.com/ahmohamed/lipidr
BugReports https://github.com/ahmohamed/lipidr/issues/
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package lipidr_2.1.2.tar.gz
Windows Binary lipidr_2.1.2.zip
Mac OS X 10.11 (El Capitan) lipidr_2.1.2.tgz
Source Repository git clone https://git.bioconductor.org/packages/lipidr
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/lipidr
Package Short Url https://bioconductor.org/packages/lipidr/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: