Package: XYomics 0.1.4

XYomics: Analysis of Sex Differences in Omics Data for Complex Diseases

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.

Authors:Enrico Glaab [aut, cre], Sophie Le Bars [aut], Mohamed Soudy [aut], Murodzhon Akhmedov [cph]

XYomics_0.1.4.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
XYomics/json (API)

# Install 'XYomics' in R:
install.packages('XYomics', repos = c('https://eglaab.r-universe.dev', 'https://cloud.r-project.org'))
Uses libs:
  • c++– GNU Standard C++ Library v3

On CRAN:

Conda:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

cpp

2.90 score 600 downloads 24 exports 212 dependencies

Last updated from:e776493453. Checks:12 OK, 1 FAIL. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64OK409
linux-devel-x86_64OK451
source / vignettesOK445
linux-release-arm64OK401
linux-release-x86_64OK398
macos-release-arm64OK301
macos-release-x86_64OK984
macos-oldrel-arm64OK378
macos-oldrel-x86_64OK545
windows-develOK433
windows-releaseOK361
windows-oldrelOK380
wasm-releaseFAIL275

Exports:call_srcategorize_sexcategorized_enrichconstruct_ppi_pcsfconvert_gene_idsgenerate_cat_reportgenerate_dotplot_scgenerate_violinplot_bulkget_string_networkget_top_hubsPCSFplot_enrichment_dotplotsplot_networkplot_network_pipelineplot_volcano_degppi_pipelinesex_interaction_analysis_bulksex_interaction_analysis_scsex_interaction_pipeline_scsex_stratified_analysis_bulksex_stratified_analysis_scsex_stratified_pipeline_scvalidate_input_bulkvalidate_input_sc

Dependencies:abindaisdkAnnotationDbiapeaplotaskpassbase64encBHBiobaseBiocGenericsBiocParallelBiostringsbitbit64bitopsblobbslibcachemcallrcaToolscliclusterclusterProfilercodetoolscommonmarkcowplotcpp11crayoncrosstalkcurldata.tableDBIDelayedArraydeldirDESeq2digestDOSEdotCall64dplyrdqrngedgeRenrichitenrichplotevaluatefarverfastDummiesfastmapfitdistrplusFNNfontawesomefontBitstreamVerafontLiberationfontquiverformatRfsfutile.loggerfutile.optionsfuturefuture.applygdtoolsgenericsGenomicRangesggforceggfunggiraphggnewscaleggplot2ggplotifyggraphggrepelggridgesggtangleggtreeglobalsglueGO.dbgoftestGOSemSimgplotsgraphlayoutsgridExtragridGraphicsgsongtablegtoolsherehighrhtmltoolshtmlwidgetshttpuvhttrhttr2icaigraphIRangesirlbaisobandjquerylibjsonliteKEGGRESTKernSmoothknitrlabelinglambda.rlaterlatticelazyevallifecyclelimmalistenvlmtestlocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemimeminiUInlmeopensslotelparallellypatchworkpbapplypillarpkgconfigplotlyplyrpngpolyclipprocessxprogressrpromisespspurrrqvalueR6RANNrappdirsRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppHNSWRcppProgressRcppTOMLreshape2reticulaterlangrmarkdownROCRrprojrootRSpectraRSQLiteRtsneS4ArraysS4VectorsS7sassscalesscattermorescatterpiesctransformSeqinfoSeuratSeuratObjectshinysitmosnowsourcetoolsspspamSparseArrayspatstat.dataspatstat.explorespatstat.geomspatstat.randomspatstat.sparsespatstat.univarspatstat.utilsstatmodstringistringrSummarizedExperimentsurvivalsyssystemfontstensortibbletidydrtidygraphtidyrtidyselecttidytreetinytextreeiotweenrutf8uwotvctrsviridisviridisLitewithrxfunxtableXVectoryamlyulab.utilszoo

Bulk RNA-Seq Example
Bulk RNA-Seq Analysis with XYomics | Introduction | Data Simulation | Differential Expression Analysis Strategies | Method 1: Sex-Stratified Analysis | Identification of Sex-Specific Genes (from Stratified Analysis) | Method 2: Interaction Term Analysis | Visualization of Expression Patterns | Pathway Enrichment Analysis | Protein-protein Interaction Network Analysis | 1. Fetching the STRING Network | 2. Constructing the PCSF Network | 3. Visualizing the Network | Generating a Report | Conclusion
Rendered fromXYomics_bulk_example.Rmdusingknitr::rmarkdown

Last update: 2026-05-11
Started: 2025-11-13

Single Cell RNA-Seq Example
Single-Cell RNA-Seq Analysis with XYomics | Introduction | Data Simulation and Preprocessing | Simulating Single-Cell Data | Preprocessing and Clustering | Annotating Cell Types and Conditions | Differential Expression Analysis Strategies | Method 1: Sex-Stratified Analysis | Method 2: Sex-Phenotype Interaction Analysis | Visualization of Gene Expression | Pathway Enrichment Analysis | Protein-protein interaction Network Analysis | Building the Network | Visualizing the Network | Generating a Report | Notes
Rendered fromXYomics_sc_example.Rmdusingknitr::rmarkdown

Last update: 2026-05-11
Started: 2025-11-13

Readme and manuals

Help Manual

Help pageTopics
Compute sex-specific differentially expressed genes (DEGs) per categorycategorize_sex
Perform Pathway Enrichment Analysis for Pre-Categorized DEGscategorized_enrich
Construct Protein-protein interaction Network using Prize-Collecting Steiner Forestconstruct_ppi_pcsf
Convert gene identifiers in a DEG tableconvert_gene_ids
Generate a Comprehensive Analysis Reportgenerate_cat_report
Generate dotplot of selected genes across groupsgenerate_dotplot_sc
Generate Violin Plots for Bulk Expression Datagenerate_violinplot_bulk
Download and Process STRING Protein-Protein Interaction Networkget_string_network
Get Top Hub Genes by Betweenness Centralityget_top_hubs
Prize-collecting Steiner Forest (PCSF)PCSF
Create enrichment dotplots from enrichResult objectsplot_enrichment_dotplots
Plot a condition-specific protein–protein interaction network with DEG annotationsplot_network
Generate protein-protein interaction network plots for single-cell DEGsplot_network_pipeline
Generate volcano plots for categorized DEGsplot_volcano_deg
Run PPI PCSf pipeline for single cell DEG categoriesppi_pipeline
Perform Sex-Phenotype Interaction Analysis for Bulk Datasex_interaction_analysis_bulk
Perform Sex-Phenotype Interaction Analysis for Single-Cell Datasex_interaction_analysis_sc
Run sex phenotype interaction analysis pipeline for single cell datasex_interaction_pipeline_sc
Perform differential expression analysis within each sexsex_stratified_analysis_bulk
Perform sex-stratified differential expression analysis for single-cell Seurat objectsex_stratified_analysis_sc
Run sex stratified differential expression pipeline for single cell datasex_stratified_pipeline_sc
Validate bulk input data for sex-stratified analysisvalidate_input_bulk
Validate single-cell input data for sex-stratified analysisvalidate_input_sc