R Observatory: Metrics for XYomics version 0.1.5

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

XYomics

0.1.5

Analysis of Sex Differences in Omics Data for Complex Diseases

0packages depend

4.1Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Enrico GlaabFirst published 2025-11-135 releasesCRAN page ↗

Tools to analyze sex differences in omics data for complex diseases. It includes functions for differential expression analysis using the 'limma' method doi:10.1093/nar/gkv007, interaction testing between sex and disease, pathway enrichment with 'clusterProfiler' doi:10.1089/omi.2011.0118, and gene regulatory network (GRN) construction and analysis using 'igraph'. The package enables a reproducible workflow from raw data processing to biological interpretation.

Install

R (CRAN)Ubuntu (r2u)

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

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

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-xyomics

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

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

Health

CRAN checks

13OK

Slowest check: 11.0 min · r-oldrel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

20

Dependencies · direct

Check history

OK2026-08-05
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-07-31
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-06-27
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-21
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 3 earlier snapshots

ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-05-14
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-03-10
11 OK · 1 NOTE · 0 WARNING · 2 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 4%

Downloads

4.1K

CRAN downloads in the past year

Rank #6,292 · ~11/day · ~342/mo

Releases R versions

Daily download trend is not available in this view yet.

35730 days

1.3K90 days

4.1K1 year

Compare downloads with other packages →

Also on318 r2u

Dependencies

Declared dependencies

31 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.6

Imports (20)

limma igraph edgeR SeuratObject Seurat data.table ggplot2 tidyrgridggraph dplyr AnnotationDbi ggrepel Rcpp cowplot patchworkmethodsDESeq2 S4Vectors clusterProfiler

LinkingTo (2)

Rcpp BH

Suggests (11)

R.utils DT gridExtra knitr htmltools kableExtra rmarkdown stringr ReactomePA org.Hs.eg.db MAST

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (4)

Maintainer (1)

Enrico Glaab

Author, Maintainer

Authors (3)

Enrico Glaab

Author, Maintainer

Sophie Le Bars

Author

Mohamed Soudy

Author

Copyright holders (1)

Murodzhon Akhmedov

Copyright holder

Package Timeline

5 releases. Pick two to compare their code metrics. R releases are shown for context.

0.1.5Latest
2026-07-30 · current release · diff ↗
0.1.4
2026-05-11 · diff ↗
R
R 4.6.0 released · 2026-04-24
0.1.3
2026-01-08 · diff ↗
0.1.2
2025-12-15 · diff ↗
0.1.1
2025-11-13
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2025-11-13
Total releases: 5 / 1 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 3.6
Download size: 4.9 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("XYomics")

Format

Glaab, E., Akhmedov, M., Le Bars, S., & Soudy, M. (2026). XYomics: Analysis of Sex Differences in Omics Data for Complex Diseases (Version 0.1.5) [Computer software]. https://doi.org/10.32614/CRAN.package.XYomics

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

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 XYomics version 0.1.5 [Data set]. HJJB, LLC. Data release v2026-08-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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