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 (3.21)
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:
Maintainer: Ahmed Mohamed <mohamed at kuicr.kyoto-u.ac.jp>
citation("lipidr")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("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")| lipidr_workflow | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Lipidomics, MassSpectrometry, Normalization, QualityControl, Software, Visualization |
| Version | 2.21.0 |
| In Bioconductor since | BioC 3.9 (R-3.6) (5.5 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/ |
See More
| 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 |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | lipidr_2.21.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| 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 |