lipidr

This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see lipidr.

Data Mining and Analysis of Lipidomics Datasets


Bioconductor version: 3.10

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 "3.6") and enter:


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

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")
lipidr_workflow HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews Lipidomics, MassSpectrometry, Normalization, QualityControl, Software, Visualization
Version 2.0.0
In Bioconductor since BioC 3.9 (R-3.6) (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
System Requirements
URL https://github.com/ahmohamed/lipidr
Bug Reports https://github.com/ahmohamed/lipidr/issues/
See More
Suggests knitr, rmarkdown, BiocStyle, ggrepel, plotly, iheatmapr, spelling, testthat
Linking To
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Build Report Build Report

Package Archives

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

Source Package lipidr_2.0.0.tar.gz
Windows Binary lipidr_2.0.0.zip
Mac OS X 10.11 (El Capitan) lipidr_2.0.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/lipidr
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/lipidr
Bioc Package Browser https://code.bioconductor.org/browse/lipidr/
Package Short Url https://bioconductor.org/packages/lipidr/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.10 Source Archive