Department of Biostatistics, Institute for Informatics, Washington University in St. Louis, St. Louis, MO 63108, USA.
Department of Biology, Indiana State University, Terre Haute, IN 47809, USA.
Bioinformatics. 2021 Dec 7;37(23):4589-4590. doi: 10.1093/bioinformatics/btab683.
Cytogenetics data, or karyotypes, are among the most common clinically used forms of genetic data. Karyotypes are stored as standardized text strings using the International System for Human Cytogenomic Nomenclature (ISCN). Historically, these data have not been used in large-scale computational analyses due to limitations in the ISCN text format and structure. Recently developed computational tools such as CytoGPS have enabled large-scale computational analyses of karyotypes. To further enable such analyses, we have now developed RCytoGPS, an R package that takes JSON files generated from CytoGPS.org and converts them into objects in R. This conversion facilitates the analysis and visualizations of karyotype data. In effect this tool streamlines the process of performing large-scale karyotype analyses, thus advancing the field of computational cytogenetic pathology.
Freely available at https://CRAN.R-project.org/package=RCytoGPS. The code for the underlying CytoGPS software can be found at https://github.com/i2-wustl/CytoGPS.
细胞遗传学数据（或核型）是最常用的临床遗传数据形式之一。核型使用国际人类细胞遗传学命名系统（ISCN）以标准化的文本字符串形式存储。由于 ISCN 文本格式和结构的限制，这些数据在过去并未用于大规模的计算分析。最近开发的计算工具，如 CytoGPS，已经实现了对核型的大规模计算分析。为了进一步支持此类分析，我们现在开发了 RCytoGPS，这是一个 R 包，它可以处理来自 CytoGPS.org 的 JSON 文件，并将其转换为 R 中的对象。这种转换便于对核型数据进行分析和可视化。实际上，该工具简化了执行大规模核型分析的过程，从而推动了计算细胞病理学领域的发展。
可在 https://CRAN.R-project.org/package=RCytoGPS 上免费获得。底层 CytoGPS 软件的代码可在 https://github.com/i2-wustl/CytoGPS 上找到。
