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GFFBase
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Getting started

  • Installation
  • Quickstart
  • Compatibility & strict modes

Using GFFBase

  • Usage Gallery — every public method, copy-pasteable
  • Analysis gallery
  • Command line
  • Connections & concurrency
  • Migrating from gffutils to gffbase
  • Cookbooks
    • GENCODE / Ensembl GTF Cookbook
    • NCBI RefSeq GFF3 Cookbook
    • MANE (Matched Annotation from NCBI and EBI) Cookbook
    • Machine Learning Workflows Cookbook

Background

  • Performance
  • Benchmark methodology
  • Datasets
  • Architecture
  • Schema v2, multipart features, and the compat/strict axis

Reference

  • API reference
  • Frequently asked questions
  • Troubleshooting
  • Citation
  • License
  • Contact

Project

  • Testing and release gates
  • Roadmap
  • Changelog
  • Contributing to GFFBase
  • Security Policy
  • Security advisory — SQL injection via order_by and set_pragmas
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Copyright © 2026, Kuan-Hao Chao
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