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Handling biological sequences in R with the bioseq package
Methods in Ecology and Evolution ( IF 6.3 ) Pub Date : 2020-09-24 , DOI: 10.1111/2041-210x.13490
François Keck 1
Affiliation  

  1. With the democratization of molecular biology, more and more ecologists are required to analyse complex datasets including biological sequences.
  2. I present the R package bioseq, a comprehensive toolset to handle biological sequences in R. The package implements three classes to work with DNA, RNA and amino acid sequences. Biological sequences are stored as simple vectors of character strings with restricted alphabets. This storage mode makes it easy to work with dataframes.
  3. The package includes a collection of functions to perform basic editing operations on sequences and biological conversion among classes. The package can read and convert data from and to several formats. Thus, users can benefit from the richness of the R environment to perform advanced biological sequence analysis.
  4. The bioseq package is a free software intended to be of significant value to researchers who need a simple and solid framework to analyse biological sequence data in R.


中文翻译:

使用bioseq包处理R中的生物序列

  1. 随着分子生物学的民主化,越来越多的生态学家需要分析包括生物学序列在内的复杂数据集。
  2. 我介绍了R包bioseq,它是处理R中生物序列的综合工具集。该包实现了三类以处理DNA,RNA和氨基酸序列。生物序列存储为带有受限字母的字符串的简单向量。这种存储模式使处理数据框变得容易。
  3. 该软件包包括一组功能,可以对序列进行基本的编辑操作并在类之间进行生物转换。该包可以读取数据并将其转换为多种格式。因此,用户可以受益于R环境的丰富性来执行高级生物序列分析。
  4. bioseq包是一个免费的软件旨在显著价值谁需要一个简单而坚实的框架来分析R.生物序列数据的研究人员
更新日期:2020-12-03
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