R Observatory: Metrics for easyLSEA version 0.2.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

easyLSEA

0.2.1Package record

Lipid Set Enrichment Analysis with Dual KS and 'fgsea' Engines

0packages depend

1.3Kdownloads / year

28.7%test coverage

13/13flavors OK

Overview

About

Maintained by David Guardamino OjedaCRAN page ↗GitHub ↗Issues ↗

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.

Install

R (CRAN)pak (dev)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("easyLSEA", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("DavidGO464/easyLSEA")

Development version from DavidGO464/easyLSEA. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-easylsea

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-easyLSEA

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-easyLSEA

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 2.8 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK7 OK2026-06-17

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.2.1

READMEYes · 673 wordsVignettesYes · 2 · dynamicNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 13
Examples that run: 100%6 run in a plain check
Exported functions with examples: 60%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 15%

Vignettes (2)

How these are measured

Downloads

1.3K

CRAN downloads in the past year

Rank #13,556 · ~4/day · ~110/mo

Releases R versions

Daily download trend is not available in this view yet.

29030 days

86190 days

1.3K1 year

Compare downloads with other packages →

Also on22 r2u6 autocran

How downloads are counted

Repository

davidgo464/easylsea ↗Account: DavidGO464

1Stars

0Forks

0Open issues

0Open PRs

2Releases

70Commits

1Commit identities

bioinformaticsenrichment-analysisfgsealipidomicslipidsmass-spectrometryr-package

70 commits · Last activity 2026-06-08 · 0% stars, 30d

Responsiveness

not measured

Stars over time

2026-07-07 · 02026-07-12 · 1

How these are measured

PracticesBeta

5 development-tooling and community-health practices detected across 4 families in the upstream repository

Checks run against github.com/davidgo464/easylsea on 2026-10-22.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel

Reproducibility and dev environment (1)

data-raw/

CRAN release process (1)

cran-comments.md

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v4 (2026-10-20)

Dependencies

Declared dependencies

8 external dependencies (excludes base and recommended)

Installing easyLSEA adds 17 packages (7 with compiled code, 14 MB of source tarballs). Heaviest: ggplot2 6.0 MB, isoband 1.5 MB, farver 1.2 MB.

Depends (1)

R >= 4.1.0

Imports (2)

ggplot2 withr

LinkingTo (0)

none

Suggests (6)

fgsea knitr openxlsx rmarkdown spelling testthat (>= 3.0.0)

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

Datasets

People & History

People (1)

David Guardamino Ojeda

Author, Maintainer since 0.2.1 (2026)

Releases (1)

0.2.1Latest
record
2026-06-16 · current release
R
R 4.6.0 released · 2026-04-24

Package metadata

First published: 2026-06-16
Total releases: 1 / 1 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.1.0
Bundled data: 4.0 KB / 1 file
Download size: 356 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("easyLSEA")

Format

Guardamino Ojeda, D. (2026). easyLSEA: Lipid Set Enrichment Analysis with Dual KS and 'fgsea' Engines (Version 0.2.1) [Computer software]. https://doi.org/10.32614/CRAN.package.easyLSEA

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for easyLSEA version 0.2.1 [Data set]. HJJB, LLC. Data release v2026-10-24. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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