rTANDEM，一个用于 MS/MS 蛋白质鉴定的 R/Bioconductor 包。
rTANDEM, an R/Bioconductor package for MS/MS protein identification.
机构信息
Proteomics Center and Department of Molecular Medicine, CHUQ Research Center, Laval University, Quebec G1V 4G2, Canada.
Proteomics Center and Department of Molecular Medicine, CHUQ Research Center, Laval University, Quebec G1V 4G2, CanadaProteomics Center and Department of Molecular Medicine, CHUQ Research Center, Laval University, Quebec G1V 4G2, Canada.
出版信息
Bioinformatics. 2014 Aug 1;30(15):2233-4. doi: 10.1093/bioinformatics/btu178. Epub 2014 Apr 3.
SUMMARY
rTANDEM is an R/Bioconductor package that interfaces the X!Tandem protein identification algorithm. The package can run the multi-threaded algorithm on proteomic data files directly from R. It also provides functions to convert search parameters and results to/from R as well as functions to manipulate parameters and automate searches. An associated R package, shinyTANDEM, provides a web-based graphical interface to visualize and interpret the results. Together, those two packages form an entry point for a general MS/MS-based proteomic pipeline in R/Bioconductor.
AVAILABILITY AND IMPLEMENTATION
rTANDEM and shinyTANDEM are distributed in R/Bioconductor, http://bioconductor.org/packages/release/bioc/. The packages are under open licenses (GPL-3 and Artistice-1.0).
CONTACT
frederic.fournier@crchuq.ulaval.ca or arnaud.droit@crchuq.ulaval.ca
SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
总结
rTANDEM 是一个 R/Bioconductor 软件包，它可以与 X!Tandem 蛋白质鉴定算法接口。该软件包可以直接从 R 运行多线程算法 proteomic 数据文件。它还提供了将搜索参数和结果转换为 R 以及操作参数和自动化搜索的功能。一个相关的 R 软件包 shinyTANDEM 提供了一个基于网络的图形界面，用于可视化和解释结果。这两个软件包共同构成了 R/Bioconductor 中基于 MS/MS 的一般蛋白质组学管道的一个入口点。
可用性和实现
rTANDEM 和 shinyTANDEM 分布在 R/Bioconductor 中，可在 http://bioconductor.org/packages/release/bioc/ 上获取。这些软件包遵循开放许可证（GPL-3 和 Artistic-1.0）。
联系方式
frederic.fournier@crchuq.ulaval.ca 或 arnaud.droit@crchuq.ulaval.ca
补充信息
补充数据可在 Bioinformatics 在线获取。
Zotero 插件