rTASSEL: an R interface to TASSEL for association mapping of complex traits
rTASSEL: an R interface to TASSEL for association mapping of complex traits
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rTASSEL：TASSEL 的 R 接口，用于复杂性状的关联映射
DOI：
10.1101/2020.07.21.209114
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发表时间：
2021
期刊：
影响因子：
--
通讯作者：
Buckler, Edward S
中科院分区：
文献类型：
--
作者：
Monier, Brandon;Casstevens, Terry M;Bradbury, Peter J;Buckler, Edward S
对于任何遗传学研究项目来说，需要有效的工具和应用程序来分析基因组多样性是必不可少的。一个这样的工具，Tassel(按关联、进化和连锁进行的特征分析)，为基因组分析提供了许多核心方法。尽管流苏的效率很高，但它在使用脚本语言进行可重复研究和与其他分析工具互动方面的手段有限。在这里，我们展示了一个R包rTASSEL，这是一个连接到各种高度使用的流苏方法和分析工具的前端。这个包的目标是创建一个统一的脚本工作流，它利用流苏的分析能力以及R流行的数据处理和解析功能，而不需要用户在这两个环境之间切换。通过实现这个工作流，我们可以获得比其他广泛使用的R包的各种功能快大约2到20倍的性能。可用性和实现rTASSEL是使用Java编写的核心流苏方法在R中实现的。RTASSEL的源代码可以在https://bitbucket.org/bucklerlab/rtassel/src/master/.上找到流苏的源代码可在https://bitbucket.org/tasseladmin/tassel-5-source/src/master/.Supplemental信息中找到rTASSEL用户手册和教程可在https://maize-genetics.github.io/rTASSEL/.免费获取有关绩效指标的补充材料可在所附文件中找到。
The need for efficient tools and applications for analyzing genomic diversity is essential for any genetics research program. One such tool, TASSEL (Trait Analysis by aSSociation, Evolution and Linkage), provides many core methods for genomic analyses. Despite its efficiency, TASSEL has limited means to use scripting languages for reproducible research and interacting with other analytical tools. Here we present an R package rTASSEL, a front-end to connect to a variety of highly used TASSEL methods and analytical tools. The goal of this package is to create a unified scripting workflow that exploits the analytical prowess of TASSEL in conjunction with R’s popular data handling and parsing capabilities without ever having the user to switch between these two environments. By implementing this workflow, we can achieve performances ranging from approximately 2 to 20 times faster than other widely used R packages for various functionalities.Availability and implementationrTASSEL is implemented in R using core TASSEL methods written in Java. The source code for rTASSEL can be found at https://bitbucket.org/bucklerlab/rtassel/src/master/. The source code for TASSEL can be found at https://bitbucket.org/tasseladmin/tassel-5-source/src/master/.Supplemental informationThe rTASSEL user manual and tutorials are freely available at https://maize-genetics.github.io/rTASSEL/. Supplemental material for this manuscript regarding performance metrics can be found in the attached file.
影响因子：
30.8
作者：
Yu, JM;Pressoir, G;Buckler, ES
通讯作者：
Buckler, ES
影响因子：
9.8
作者：
Zhu, Zhihong;Bakshi, Andrew;Yang, Jian
通讯作者：
Yang, Jian
DOI：
10.1534/g3.112.004259
发表时间：
2012-11
期刊：
G3 (Bethesda, Md.)
影响因子：
--
作者：
Endelman JB;Jannink JL
通讯作者：
Jannink JL