v1.11.0 Release

[1.11.0] - 2025-05-27

Published

• 🎉 SEgene paper officially published:
  • Shinkai, N., Asada, K., Machino, H., Takasawa, K., Takahashi, S., Kouno, N., Komatsu, M., Hamamoto, R., & Kaneko, S. (2025). SEgene identifies links between super enhancers and gene expression across cell types. npj Systems Biology and Applications, 11(1), 49. https://doi.org/10.1038/s41540-025-00533-x
  • Test data and supplementary materials released on Figshare: https://doi.org/10.6084/m9.figshare.28171127

Changed

• Documentation updated following paper publication:
  • Updated all README files to include the official paper citation
  • Replaced all "manuscript in preparation" notices with published paper information
  • Updated CITATION file with complete publication details and BibTeX format
  • Standardized citation section titles in Japanese READMEs to "引用 / Citation"
  • Updated Figshare links throughout documentation from placeholders to official DOI

Added

• Citation sections: Added missing citation sections to ensure all components include proper citation information