XYomics
Analysis of Sex Differences in Omics Data for Complex Diseases
v0.1.3
·
Jan 8, 2026
·
MIT + file LICENSE
Description
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.
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CRAN Check Status
2
ERROR
1
NOTE
11
OK
Show all 14 flavors
| Flavor | Status |
|---|---|
| r-devel-linux-x86_64-debian-clang | OK |
| r-devel-linux-x86_64-debian-gcc | OK |
| r-devel-linux-x86_64-fedora-clang | OK |
| r-devel-linux-x86_64-fedora-gcc | OK |
| r-devel-macos-arm64 | ERROR |
| r-devel-windows-x86_64 | OK |
| r-oldrel-macos-arm64 | ERROR |
| r-oldrel-macos-x86_64 | NOTE |
| r-oldrel-windows-x86_64 | OK |
| r-patched-linux-x86_64 | OK |
| r-release-linux-x86_64 | OK |
| r-release-macos-arm64 | OK |
| r-release-macos-x86_64 | OK |
| r-release-windows-x86_64 | OK |
Check details (3 non-OK)
ERROR
r-devel-macos-arm64
re-building of vignette outputs
Error(s) in re-building vignettes:
--- re-building ‘XYomics_bulk_example.Rmd’ using rmarkdown
Quitting from XYomics_bulk_example.Rmd:206-240 [pathway-analysis]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `get()`:
! invalid 'envir' argument
---
Backtrace:
▆
1. └─XYomics::improved_pathway_enrichment(...)
2. └─clusterProfiler::enrichGO(...)
3. └─clusterProfiler:::add_GO_Ontology(res, GO_DATA)
4. └─base::get("GO2ONT", envir = GO_DATA)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'XYomics_bulk_example.Rmd' failed with diagnostics:
invalid 'envir' argument
--- failed re-building ‘XYomics_bulk_example.Rmd’
--- re-building ‘XYomics_sc_example.Rmd’ using rmarkdown
Performing log-normalization
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[----|----|----|----|----|----|----|----|----|----|
************************************************
...[truncated]...
s
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|
|
| | 0%
|
|======================================================================| 100%
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Using method 'umap'
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
--- finished re-building ‘XYomics_sc_example.Rmd’
SUMMARY: processing the following file failed:
‘XYomics_bulk_example.Rmd’
Error: Vignette re-building failed.
Execution halted
ERROR
r-oldrel-macos-arm64
whether package can be installed
Installation failed. See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.4/XYomics.Rcheck/00install.out’ for details.
NOTE
r-oldrel-macos-x86_64
installed package size
installed size is 5.4Mb
sub-directories of 1Mb or more:
doc 2.1Mb
libs 2.2Mb
Check History
ERROR 11 OK · 1 NOTE · 0 WARNING · 2 ERROR · 0 FAILURE Mar 10, 2026
ERROR
r-patched-linux-x86_64
package dependencies
Package required but not available: ‘clusterProfiler’ See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual.
ERROR
r-oldrel-macos-arm64
whether package can be installed
Installation failed. See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.4/XYomics.Rcheck/00install.out’ for details.
NOTE
r-oldrel-macos-x86_64
installed package size
installed size is 5.4Mb
sub-directories of 1Mb or more:
doc 2.1Mb
libs 2.2Mb