Bioframe: operations on genomic intervals in Pandas dataframes.
Bioframe: operations on genomic intervals in Pandas dataframes.
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Bioframe：对 Pandas 数据框中的基因组间隔进行操作。
DOI：
10.1093/bioinformatics/btae088
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发表时间：
2024
期刊：
影响因子：
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通讯作者：
Venev,Sergey
中科院分区：
文献类型：
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作者：
Open2C;Abdennur,Nezar;Fudenberg,Geoffrey;Flyamer,IlyaM;Galitsyna,AleksandraA;Goloborodko,Anton;Imakaev,Maxim;Venev,Sergey
基因组间隔是计算基因组生物学中最流行的数据结构之一，用于表示从基因到DNA结合位点到疾病变体的特征。对基因组间隔的操作提供了一种语言，用于询问有关特征之间关系的问题。虽然有很好的命令行区间算术工具，但它们并不能顺利地集成到Python中，最受欢迎的通用计算和可视化环境之一。结果Bioframe是一个库，可以在Python中对基因组间隔框架进行灵活和高性能的操作。Bioframe通过直接在两个最常见的-使用Python库NumPyandPandas。BioframeAPI支持灵活的名称和列顺序，并从数据格式中分离操作，以避免不必要的转换，这是生物信息学家的常见问题。BioframeAPI实现了这些目标，同时保持了高性能和丰富的功能集。可用性和实现BioframeAPI是MIT许可下的开源，跨平台，可以从Python包索引安装。源代码由GitHub上的Open 2C维护，网址为https://github.com/open2c/bioframe。
MotivationGenomic 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.ResultsBioframeis a library to enable flexible and performant operations on genomic interval dataframes in Python.Bioframeextends 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,NumPyandPandas. ThebioframeAPI enables flexible name and column orders, and decouples operations from data formats to avoid unnecessary conversions, a common scourge for bioinformaticians.Bioframeachieves these goals while maintaining high performance and a rich set of features.Availability and implementationBioframeis 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.