v1.10.0 Release

[1.10.0] - 2025-05-02

Added

• Enhanced SEgene_peakprep with edgeR normalized CPM:
  • Added edgeR normalized CPM (calcnorm CPM) as the third quantification method in addition to Standard log2-CPM and BigWig methods
  • Implemented integration with R's edgeR package via rpy2 for advanced normalization of ChIP-seq count data
  • Added multiple normalization methods from edgeR: upperquartile (default), TMM, RLE
  • Implemented optional filtering capabilities based on CPM values across samples
  • Added comprehensive documentation in both English and Japanese
  • Created a dedicated edgeR normalized CPM guide (cpm_calcnorm_README.md)

Changed

• Updated SEgene_peakprep code and documentation:
  • Reorganized CPM method to support both standard log2-CPM and edgeR normalized CPM calculations
  • Updated command-line interface with new --calcnorm parameter and related options for normalization control
  • Improved sample name handling for better compatibility with complex file naming conventions
  • Updated all relevant documentation (README.md, README_ja.md, cpm_README.md, cpm_README_ja.md) to explain the new capabilities
• Dependencies:
  • Added R (≥4.2.0), edgeR (≥3.40.0), and rpy2 (≥3.5.0) as new dependencies for the edgeR normalized CPM functionality
  • Updated installation instructions to explain the setup of R and Bioconductor environments