Package: easyLSEA 0.2.1
David Guardamino Ojeda
easyLSEA: Lipid Set Enrichment Analysis with Dual KS and 'fgsea' Engines
Provides biology-aware lipid set enrichment analysis (LSEA) for lipidomics data using dual engines: the Kolmogorov-Smirnov test and the fast gene set enrichment algorithm from the 'fgsea' package. Annotates lipids into biological groups at three levels (lipid class, LIPID MAPS category, functional category) and tests for coordinated directional shifts between conditions. Includes fatty acid chain analysis with trend plots weighted by lipid abundance (Spearman rank correlation, configurable smoothing), wide-format chain position output (sn-1, sn-2, sn-3, sn-4), annotation confidence filtering, and export utilities for reproducible reporting in CSV, 'Excel', and PDF formats. Vignettes are available in English and Spanish. Methods are based on Subramanian et al. (2005) <doi:10.1073/pnas.0506580102> and Korotkevich et al. (2021) <doi:10.1101/060012>.
Authors:
easyLSEA_0.2.1.tar.gz
easyLSEA_0.2.1.tar.gz(r-4.7-any)easyLSEA_0.2.1.tar.gz(r-4.6-any)
easyLSEA_0.2.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
easyLSEA/json (API)
| # Install 'easyLSEA' in R: |
| install.packages('easyLSEA', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/davidgo464/easylsea/issues
- lipid_example - Example lipidomics dataset
Last updated from:70cad577df. Checks:4 OK. Indexed: no.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 168 | ||
| source / vignettes | OK | 359 | ||
| linux-release-x86_64 | OK | 170 | ||
| wasm-release | OK | 133 |
Exports:annotate_lipidannotate_lipidsdefault_chain_configeasyLSEAexport_lseaparse_lipid_chainsplot_chainsplot_distributionplot_lsearun_lsea
Dependencies:clicpp11farverggplot2gluegtableisobandlabelinglifecycleR6RColorBrewerrlangS7scalesvctrsviridisLitewithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Annotate lipid names with LIPID MAPS classification | annotate_lipid |
| Annotate lipid names with class and category information | annotate_lipids |
| Default chain analysis class configuration | default_chain_config |
| Lipid Set Enrichment Analysis — full pipeline | easyLSEA |
| Export easyLSEA results to disk | export_lsea |
| Example lipidomics dataset | lipid_example |
| Parse acyl chain composition from a lipidomics data.frame | parse_lipid_chains |
| Generate chain analysis plots | plot_chains |
| Distribution enrichment boxplot per lipid set | plot_distribution |
| Generate LSEA enrichment plots | plot_lsea |
| Print method for easyLSEA_result | print.easyLSEA_result |
| Lipid Set Enrichment Analysis | run_lsea |
| Summary method for easyLSEA_result | summary.easyLSEA_result |
