segene - v1.13.0 Release

[1.13.0] - 2025-07-23

Added

• New development version: SEgeneanalyzererna:
  • eRNAbase-specific analysis tool derived from SEgeneregionpackage
  • Command-line interface with 4 specialized commands: report, single, batch, prepare-stats
  • pip-installable package with erna-analyzer system-wide command
  • Support for multiple BED files and Parquet metadata format specific to eRNAbase
  • Species filtering functionality (human/mouse) for eRNAbase datasets
  • Comprehensive bilingual documentation (English and Japanese)
  • Enhanced chromosome filtering and validation for genomic region analysis
  • WSL-compatible matplotlib backend configuration for headless environments
  • Complete test suite with real eRNAbase data validation (858 samples)
  • Statistical enrichment analysis with Fisher's exact test and FDR correction
  • Multiple output formats: PNG, SVG, PDF, CSV, HTML reports
  • Positioned as eRNAbase-specialized counterpart to SEgene_analyzer

Changed

• Documentation updates:
  • Added SEgeneanalyzererna to "Development Versions" section in main README files
  • Updated usage links to include the new development version documentation

- Python
Published by nswork168 11 months ago

segene - v1.12.0 Release

[1.12.0] - 2025-07-18

Added

• New development version: SEgene_analyzer:
  • Development version of SEgeneregionanalyzer with enhanced CLI interface and modern Python packaging
  • Command-line interface with 4 specialized commands: prepare-stats, batch, single, report
  • pip-installable package with sedb-analyzer system-wide command
  • Advanced caching system for improved batch processing performance
  • Comprehensive bilingual documentation (English and Japanese)
  • Test suite with 29 test cases covering core functionality
  • Enhanced matplotlib backend configuration for WSL environments
  • Multiple output formats: PNG, SVG, PDF, EPS
  • Positioned as experimental development version alongside stable SEgeneregionanalyzer

Changed

• Documentation structure updates:
  • Added "Development Versions" section to main README files
  • Updated Program Structure section to mention development versions availability
  • Enhanced README files with bold emphasis on development program information
  • Improved navigation with direct links to development version documentation

- Python
Published by nswork168 11 months ago

segene - 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

- Python
Published by nswork168 about 1 year ago

segene - 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 (cpmcalcnormREADME.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, READMEja.md, cpmREADME.md, cpmREADMEja.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

- Python
Published by nswork168 about 1 year ago

segene - 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 SEgenepeakprep and SEgenegeneprep 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

- Python
Published by nswork168 about 1 year ago

segene - v1.8.0 Release

[1.8.0] - 2025-04-17

Added

• Enhanced SEgene_peakprep with differential analysis:
  • Added differential analysis functionality for ChIP-seq versus Input control data within the bigWig processing workflow.
  • This feature utilizes bamCompare from the deeptools suite to identify significantly enriched regions by comparing ChIP signals against Input signals.

Changed

• Updated SEgene_peakprep code and documentation:
  • Updated relevant scripts within the SEgene_peakprep directory (including bigwig_peakprep_bamdiff.py, bigwig_peakprep_bamdiff_utils.py, bigwig_peakprep.py, etc.) to integrate the new differential analysis capability.
  • Correspondingly revised associated documentation (README.md, README_ja.md, bigwig_README.md, bigwig_README_ja.md) to accurately reflect the updated features and their usage instructions.

- Python
Published by nswork168 about 1 year ago

segene - 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 "mergeSV.tsv" format from v1.6.1, which should correctly be "mergeSE.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

- Python
Published by nswork168 about 1 year ago

segene - v1.6.1 Release

[1.6.1] - 2025-04-11

Added

• SEgene_peakprep improvements:
  • Added direct support for BED and merge_SV.tsv input formats in annotation files
  • Automatic conversion of BED and merge_SV formats to SAF format internally
  • Added --is_mergesv_format flag for specifying merge_SV.tsv format annotations

Changed

• SEgene_peakprep workflow optimization:
  • Streamlined command-line interface with more intuitive parameter names
  • Adjusted log level output for better readability during execution
  • Improved temporary file handling
• Documentation updates:
  • Comprehensive revision of README files (both English and Japanese)
  • Added clearer examples for different annotation file formats
  • Updated command examples to reflect the new parameter structure
  • Improved troubleshooting section

- Python
Published by nswork168 about 1 year ago

segene - v1.6.0 Release

[1.6.0] - 2025-04-06

Added

• New component: SEgene_peakprep:
  • New data preprocessing pipeline for ChIP-seq data normalization
  • Integrated processing of peak region information from multiple BAM files into normalized data tables
  • Calculation of total mapped reads using samtools flagstat
  • Read counting in genomic regions using featureCounts
  • CPM calculation and log transformation functionality
  • Integration with existing workflow components
• Documentation:
  • Documentation for SEgene_peakprep
  • Revised workflow description positioning SEgene_peakprep as the initial data preparation step

- Python
Published by nswork168 about 1 year ago

segene - v1.5.0 Release

[1.5.0] - 2025-04-05

Added

• New component: SEgene_RegionAnalyzer:
  • Added a new analytical tool for evaluating super-enhancer activity in genomic regions of interest
  • Integrated with public databases (currently SEdb 2.0)
  • Performs enrichment analysis of tissue-specific super-enhancer associations
  • Supports both SEgene output TSV files and standard BED format inputs
  • Generates comprehensive TSV reports and visual HTML outputs
• Documentation:
  • Added detailed documentation for SEgene_RegionAnalyzer
  • Updated main README to include the new component in the project structure

Changed

• Reorganized the project structure to include SEgene_RegionAnalyzer as an optional component
• Updated the workflow description to reflect the extended analytical capabilities

- Python
Published by nswork168 about 1 year ago

segene - v1.4.0 Release

[1.4.0] - 2025-03-19

Added

• Enhanced network visualization capabilities:
  • Added detailed graph drawing methods (draw_network_detailed, draw_subnetwork_detailed, draw_two_layer_subnetwork_detailed)
  • Added support for multiple output formats (SVG, PNG, EPS, PDF) across all visualization functions
  • Added customization options for node styling, edge styling, and subgraph boundaries
• Improved data export functionality:
  • Added ability to save graph data alongside visualizations
  • Added logging capabilities for reproducibility
  • Added support for exporting data in various formats (CSV, TSV, JSON)
• Enhanced visualization parameters:
  • Added resolution (DPI) control for raster format outputs
  • Added figure size and styling customization options
  • Added custom title support for all network visualization methods (draw_network, draw_subnetwork, draw_two_layer_subnetwork)

Changed

• Updated existing visualization methods to support expanded format options
• Extended graph rendering interfaces with additional customization parameters
• Improved file naming and organization for saved outputs

Notes

• These visualization enhancements are designed to maintain compatibility with existing network analysis functions

Full Changelog: https://github.com/hamamoto-lab/SEgene/compare/v1.3.0...v1.4.0

- Python
Published by nswork168 about 1 year ago

segene - v1.3.0 Release

[1.3.0] - 2025-03-15

Added

• Enhanced visualization options for ROSE summary plots:
  • Added customizable parameters for DPI, figure size, and output format
  • Improved figure saving capabilities with format selection

Fixed

• Fixed threshold comparison in p2gl_path_to_filter_df function to correct filtering behavior

Notes

• Added pronunciation guide for SEgene ("S-E-gene") in documentation

Full Changelog: https://github.com/hamamoto-lab/SEgene/compare/v1.2.0...v1.3.0

- Python
Published by nswork168 over 1 year ago

segene - v1.2.0 Release

[1.2.0] - 2025-03-11

Added

• New core analysis capabilities for SE rank distribution:
  • Added functionality to search for gene-linked super-enhancers across multiple samples
  • Implemented super-enhancer ranking analysis within datasets
  • Developed statistical tools for percentile calculation and distribution analysis
  • Created visualization methods for SE rank distributions across samples
• New tutorial notebooks to demonstrate the new analysis features:
  • tutorial_book_SE_rank_disribution.ipynb (English)
  • tutorial_book_SE_rank_disribution_ja.ipynb (Japanese)
  • These notebooks guide users through analyzing the ranking status (position and percentile) of super-enhancers corresponding to specific genes

Notes

• Documentation in README files has been updated to include information about the new notebooks

- Python
Published by nswork168 over 1 year ago

segene - v1.1.0 Release

[1.1.0] - 2025-02-07

Added

• New CLI tools (cli_tools/) for streamlined featureCounts processing, CPM calculation, and SE–gene correlation analysis
  • Scripts such as generate_gtf.py, generate_file_list.sh, run_featurecounts_array.sh, etc.
  • correlation_analysis.py computes Pearson correlation between SE (CPM) and genes (TPM)
• Documentation updates:
  • Added English (README.md) and Japanese (README_ja.md) documentation under /cli_tools/
  • Updated the main repository documentation (README.md) and /SE_to_gene_links/ docs to explain how to integrate the new CLI tools

Changed

• Refined repository structure by separating stand-alone CLI scripts into cli_tools/, independent of SEgene_package

Notes

• The newly added documents provide usage instructions and workflow details in both English and Japanese
  
• Enables advanced or extended analyses on top of the existing SE_to_gene_links functionalities

- Python
Published by nswork168 over 1 year ago

segene - v1.0.0 Initial Release

v1.0.0 Release Notes

We are excited to announce the initial release of SEgene, a comprehensive platform for identifying and analyzing Super-Enhancer-to-gene links through statistical approaches. This release marks the foundation of a toolset that will enable researchers to explore gene regulation with greater insight.

Detailed Functionality

• peaktogene_links

  • Retrieves correlation information between gene expression and enhancer peaks.
  • Supports data analysis and visualization.

• SEtogene_links

  • Evaluates and analyzes super-enhancer to gene links using correlation data from peak_to_gene_links.
  • Utilizes graph theory for data visualization and interactive analysis with Jupyter Notebook.

For detailed installation instructions and documentation, please visit our GitHub repository.

Full Changelog: https://github.com/hamamoto-lab/SEgene/commits/v1.0.0

- Python
Published by nswork168 over 1 year ago