v1.9.0 Release

[1.9.0] - 2025-04-24

Added

• New component: SEgene_geneprep:
  • Preparation tool for RNA-seq input data to add region information for P2GL input formats
  • Extracts gene position information from GTF files and merges with expression data from TPM files
  • Converts salmon output from nf-core/rnaseq pipeline to CSV format suitable for RNAinput in SEgene analysis
  • Supports multiple input formats including standard GTF and salmon TPM files
  • Compatible with genome annotations from Illumina iGenomes (e.g., GRCh38)
  • Comprehensive documentation in both English and Japanese
• Workflow visualization:
  • Added mermaid diagrams to visualize the complete SEgene workflow
  • Clear illustration of the four-step process: P2GL Preparation, P2GL Analysis, SE Analysis, and Region Evaluation

Changed

• Program structure reorganization:
  • Reorganized workflow into four primary components for clearer understanding
  • Positioned SEgene_peakprep and SEgene_geneprep as the initial P2GL data preparation steps
  • Updated documentation structure to reflect the new workflow organization
• Documentation updates:
  • Comprehensive revision of main README files (both English and Japanese)
  • Restructured program structure sections for better clarity
  • Enhanced descriptions of component relationships and data flow