LIPIDIFy
This is the development version of LIPIDIFy; to use it, please install the devel version of Bioconductor.
Comprehensive Lipidomics Data Analysis with Interactive Visualization
Bioconductor version: Development (3.24)
Provides a comprehensive toolkit for end-to-end lipidomics data analysis, including missing value imputation, batch effect correction, normalization, differential abundance analysis using limma and edgeR, gene set enrichment analysis, and extensive visualization capabilities. Lipid names are automatically classified by class, subclass, and fatty-acid saturation. Features both an interactive Shiny interface for bench biologists and fully scriptable R functions for bioinformaticians. Supports flexible custom lipid classification schemes and user-defined enrichment sets.
Author: Fayrouz Hammal [aut, cre]
, Karen Sheppard [fnd] (NHMRC of Australia grant #2020050)
Maintainer: Fayrouz Hammal <fayrouz.hammal at petermac.org>
citation("LIPIDIFy")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
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("LIPIDIFy")
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("LIPIDIFy")| LIPIDIFy | HTML | R Script |
| Reference Manual |
Details
| biocViews | BatchEffect, Classification, DataImport, DifferentialExpression, GeneSetEnrichment, Lipidomics, MassSpectrometry, MultipleComparison, Normalization, Preprocessing, QualityControl, ShinyApps, Software, Visualization |
| Version | 0.99.7 |
| In Bioconductor since | BioC 3.24 (R-4.6) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.5.0) |
| Imports | shiny (>= 1.8.0), shinydashboard, ggplot2 (>= 3.5.0), ggrepel, plotly, DT, tidyr, dplyr, scales, gridExtra, grid, pheatmap, limma, edgeR, fgsea, FactoMineR, pls, openxlsx, rmarkdown, stringr, withr, utils, stats, grDevices |
| System Requirements | |
| URL | https://github.com/fayrouzhammal/LIPIDIFy |
| Bug Reports | https://github.com/fayrouzhammal/LIPIDIFy/issues |
See More
| Suggests | BiocStyle, knitr, testthat (>= 3.0.0), impute, sva, vsn, SummarizedExperiment, tinytex, shinytest2, chromote |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | LIPIDIFy_0.99.7.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | LIPIDIFy_0.99.7.tgz |
| macOS Binary (sonoma-arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/LIPIDIFy |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/LIPIDIFy |
| Bioc Package Browser | https://code.bioconductor.org/browse/LIPIDIFy/ |
| Package Short Url | https://bioconductor.org/packages/LIPIDIFy/ |
| Package Downloads Report | Download Stats |