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Bioframe: operations on genomic intervals in Pandas dataframes.

Authors :
Abdennur, Nezar
Fudenberg, Geoffrey
Flyamer, Ilya M
Galitsyna, Aleksandra A
Goloborodko, Anton
Imakaev, Maxim
Venev, Sergey
Source :
Bioinformatics. Feb2024, Vol. 40 Issue 2, p1-4. 4p.
Publication Year :
2024

Abstract

Motivation Genomic intervals are one of the most prevalent data structures in computational genome biology, and used to represent features ranging from genes, to DNA binding sites, to disease variants. Operations on genomic intervals provide a language for asking questions about relationships between features. While there are excellent interval arithmetic tools for the command line, they are not smoothly integrated into Python, one of the most popular general-purpose computational and visualization environments. Results Bioframe is a library to enable flexible and performant operations on genomic interval dataframes in Python. Bioframe extends the Python data science stack to use cases for computational genome biology by building directly on top of two of the most commonly-used Python libraries, NumPy and Pandas. The bioframe API enables flexible name and column orders, and decouples operations from data formats to avoid unnecessary conversions, a common scourge for bioinformaticians. Bioframe achieves these goals while maintaining high performance and a rich set of features. Availability and implementation Bioframe is open-source under MIT license, cross-platform, and can be installed from the Python Package Index. The source code is maintained by Open2C on GitHub at https://github.com/open2c/bioframe. [ABSTRACT FROM AUTHOR]

Details

Language :
English
ISSN :
13674803
Volume :
40
Issue :
2
Database :
Academic Search Index
Journal :
Bioinformatics
Publication Type :
Academic Journal
Accession number :
175802045
Full Text :
https://doi.org/10.1093/bioinformatics/btae088