Bioframe

Bioframe extends the Python data science stack by building upon NumPy and Pandas to enable flexible and performant operations on genomic interval dataframes for computational genome biology.

Key Features:

• Flexible API: The bioframe API enables flexible name and column orders, and decouples operations from data formats to avoid unnecessary conversions.
• High Performance: Bioframe maintains high performance while providing a rich set of features for genomic interval operations.
• Direct Integration: Bioframe builds directly on top of NumPy and Pandas, two of the most commonly-used Python libraries, for smooth integration into Python computational and visualization environments.

Scientific Applications:

• Genomic Feature Analysis: Bioframe supports operations on genomic intervals representing features ranging from genes, to DNA binding sites, to disease variants.
• Interval Arithmetic: Bioframe provides a language for asking questions about relationships between genomic features through interval operations.

Methodology:

Bioframe builds directly on top of NumPy and Pandas, with an API that decouples operations from data formats and enables flexible name and column orders.