R Observatory: Metrics for XYomics version 0.1.5

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

XYomics

0.1.5Package record

Analysis of Sex Differences in Omics Data for Complex Diseases

0packages depend

4.7Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Enrico GlaabCRAN 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. 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

Health

CRAN checks

13OK

Additional issues

CRAN check page ↗

Slowest check: 10.7 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-09-08
ERROR12 OK, 1 ERROR2026-09-07
OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-07-31
OK13 OK2026-06-27

Show 5 earlier changesHide 5 earlier changes

ERROR12 OK, 1 ERROR2026-06-21
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
OK13 OK2026-05-14
ERROR11 OK, 1 NOTE, 2 ERROR2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.1.5

READMENoVignettesYes · 2 · dynamicNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 25 (2 internal)includes a package overview page
Examples that run: 100%1 run in a plain check
Exported functions with examples: 4%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 4%

Vignettes (2)

How these are measured

Downloads

4.7K

CRAN downloads in the past year

Rank #10,377 · ~13/day · ~394/mo

Releases R versions

Daily download trend is not available in this view yet.

33330 days

97290 days

4.7K1 year

Compare downloads with other packages →

Also on348 r2u

How downloads are counted

Dependencies

Declared dependencies

31 external dependencies (excludes base and recommended)

Installing XYomics adds 142 packages (87 with compiled code, 138 MB of source tarballs). Heaviest: BH 14 MB, stringi 11 MB, ggplot2 6.0 MB. 6 more not on CRAN are not measured.

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.

How these are counted

Code & Tests

Datasets

People & History

People (4)

Enrico Glaab

Author, Maintainer since 0.1.1 (2025)

Sophie Le Bars

Author

Mohamed Soudy

Author

Murodzhon Akhmedov

Copyright holder

Releases (5)

Pick two releases to compare their code metrics.

0.1.5Latest
record
2026-07-30 · current release · diff ↗
0.1.4
record
2026-05-11 · diff ↗ ·
removed 8 exports
categorize_sex_sc, categorized_enrich_sc, convertdf2enr, generate_boxplot, generate_report, identify_sex_specific_genes, improved_pathway_enrichment, visualize_network

added 14 exports
categorize_sex, categorized_enrich, convert_gene_ids, generate_dotplot_sc, generate_violinplot_bulk, get_top_hubs, plot_enrichment_dotplots, plot_network_pipeline, plot_volcano_deg, ppi_pipeline, sex_interaction_pipeline_sc, sex_stratified_pipeline_sc, validate_input_bulk, validate_input_sc
R
R 4.6.0 released · 2026-04-24
0.1.3
record
2026-01-08 · diff ↗
0.1.2
record
2025-12-15 · diff ↗
0.1.1
record
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

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 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 XYomics version 0.1.5 [Data set]. HJJB, LLC. Data release v2026-10-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

Report a problem with this page →