lipidr

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

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9

Data Mining and Analysis of Lipidomics Datasets

Bioconductor version: Development (3.24)

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, total chain length and unsaturation.

Author: Ahmed Mohamed [cre] ORCID: 0000-0001-6507-5300 , Ahmed Mohamed [aut], Jeffrey Molendijk [aut]

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

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

Ahmed Mohamed, Jeffrey Molendijk. lipidr: Data Mining and Analysis of Lipidomics Datasets. doi:10.18129/B9.bioc.lipidr, R package version 2.27.0, https://bioconductor.org/packages/lipidr.

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("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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Lipidomics, MassSpectrometry, Normalization, QualityControl, Software, Visualization
Version	2.27.0
In Bioconductor since	BioC 3.9 (R-3.6) (7.5 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, imputeLCMD, magrittr
System Requirements
URL	https://github.com/ahmohamed/lipidr
Bug Reports	https://github.com/ahmohamed/lipidr/issues/

Suggests	knitr, rmarkdown, BiocStyle, ggrepel, plotly, spelling, testthat
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me	rgoslin
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	lipidr_2.27.0.tar.gz
Windows Binary (x86_64)
macOS Binary (big-sur-x86_64)	lipidr_2.27.0.tgz
macOS Binary (sonoma-arm64)	lipidr_2.27.0.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