Changelog

All notable changes to gs2txt will be documented in this page.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

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Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

Unreleased

0.1.0 - 2025-01-13

Added

• Core Features
• GeneSetAnnotator - Main annotation engine for gene set analysis
• Built-in gene filtering by p-value and log2FC thresholds
• Automatic pathway enrichment using GSEApy

• Customizable prompt templates for domain-specific use cases

• LLM Providers

• OpenAIProvider - OpenAI API integration (GPT-4, GPT-3.5)
• AnthropicProvider - Anthropic Claude integration

• LiteLLMProvider - Unified interface for multiple LLM backends

• Enrichment Methods

• PathwayEnrichment - GSEApy-based enrichment (MSigDB, KEGG, GO)

• CustomEnrichment - Adapter for pre-computed results

• Batch Processing

• BatchProcessor - Process multiple gene sets from CSV files
• Support for grouped data (e.g., by cluster)

• Automatic output formatting (gs, annotation columns)

• Two-Stage Pipeline (New in 0.1.0)

• TwoStagePipeline.preprocess() - Single file preprocessing
• TwoStagePipeline.preprocess_batch() - Batch preprocessing from folders
• TwoStagePipeline.annotate() - LLM annotation stage
• YAML configuration support

• Multiple pathway source merging (GO, KEGG, Reactome)

• CLI Interface

• gs2txt command for processing CSV files
• Support for multiple providers and models

• Configurable filtering parameters

• Documentation

• Three usage scenarios with example scripts
• Comprehensive README with API examples
• MkDocs documentation site

Example Scripts

• scenario1_batch_csv.py - Batch CSV processing
• scenario2_api.py - Python API integration
• scenario3_two_stage.py - Two-stage pipeline processing

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