v1.7.0 Release

[1.7.0] - 2025-04-14

Added

• New BigWig method in SEgene_peakprep:
  • Implemented a new alternative approach for peak quantification using BigWig files
  • Added deeptools integration for BAM to BigWig conversion and signal quantification
  • Added bamCoverage functionality with multiple normalization options (RPGC, CPM, BPM, RPKM)
  • Added multiBigwigSummary processing for extracting signal values from specified regions
  • Implemented automatic log2 transformation of signal values
  • Created comprehensive utilities for processing and handling BigWig files and genomic coordinates
• Enhanced processing workflow:
  • Added three-stage workflow with separate scripts for different processing steps
  • Added wrapper script for seamless execution of the entire pipeline
  • Added option to run individual processing steps separately

Changed

• Expanded SEgene_peakprep capabilities:
  • Updated documentation to reflect both CPM and BigWig implementation methods
  • Expanded command-line interface to support both processing approaches
  • Standardized output formats across both methods for downstream compatibility

Fixed

• Corrected terminology in SEgene_peakprep:
  • Fixed references to "merge_SV.tsv" format from v1.6.1, which should correctly be "merge_SE.tsv" (Super-Enhancer) format
  • Updated all related documentation and code comments to use consistent terminology
  • Fixed --is_mergesv_format flag name to --is_mergese_format for specifying merge_SE.tsv format annotations