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GMIEC: a shiny application for the identification of gene-targeted drugs for precision medicine.
BMC Genomics ( IF 3.5 ) Pub Date : 2020-09-10 , DOI: 10.1186/s12864-020-06996-y
Guidantonio Malagoli Tagliazucchi 1, 2 , Cristian Taccioli 3
Affiliation  

Precision medicine is a medical approach that takes into account individual genetic variability and often requires Next Generation Sequencing data in order to predict new treatments. Here we present GMIEC, Genomic Modules Identification et Characterization for genomics medicine, an application that is able to identify specific drugs at the level of single patient integrating multi-omics data such as RNA-sequencing, copy-number variation, methylation, Chromatin Immuno-Precipitation and Exome/Whole Genome sequencing. It is also possible to include clinical data related to each patient. GMIEC has been developed as a web-based R-Shiny platform and gives as output a table easy to use and explore. We present GMIEC, a Shiny application for genomics medicine. The tool allows the users the integration of two or more multiple omics datasets (e.g. gene-expression, copy-number), at sample level, to identify groups of genes that share common genomic and corresponding drugs. We demonstrate the characteristics of our application by using it to analyze a prostate cancer data set. GMIEC provides a simple interface for genomics medicine. GMIEC was develop with Shiny to provide an application that does not require advanced programming skills. GMIEC consists of three sub-application for the analysis (GMIEC-AN), the visualization (GMIEC-VIS) and the exploration of results (GMIEC-RES). GMIEC is an open source software and is available at https://github.com/guidmt/GMIEC-shiny

中文翻译:

GMIEC:鉴定精密医学中基因靶向药物的闪亮应用。

精密医学是一种考虑到个体遗传​​变异性的医学方法,通常需要下一代测序数据才能预测新的治疗方法。在这里,我们介绍了GMIEC,基因组学医学的基因组模块识别和表征,该应用程序能够在单个患者的水平上结合多组学数据(例如RNA测序,拷贝数变异,甲基化,染色质免疫-沉淀和外显子组/全基因组测序。也可以包括与每个患者有关的临床数据。GMIEC已开发为基于Web的R-Shiny平台,并为输出提供了易于使用和浏览的表格。我们介绍了GMIEC,这是一种用于基因组医学的闪亮应用程序。该工具允许用户集成两个或多个多重组学数据集(例如 基因表达,拷贝数),以样品水平鉴定共享共同基因组和相应药物的基因组。我们通过使用它来分析前列腺癌数据集来演示我们应用程序的特征。GMIEC为基因组医学提供了一个简单的界面。GMIEC与Shiny一起开发,旨在提供不需要高级编程技能的应用程序。GMIEC包括三个子应用程序,分别用于分析(GMIEC-AN),可视化(GMIEC-VIS)和结果探索(GMIEC-RES)。GMIEC是一种开源软件,可从https://github.com/guidmt/GMIEC-shiny获得。GMIEC为基因组医学提供了一个简单的界面。GMIEC与Shiny一起开发,旨在提供不需要高级编程技能的应用程序。GMIEC包括三个子应用程序,分别用于分析(GMIEC-AN),可视化(GMIEC-VIS)和结果探索(GMIEC-RES)。GMIEC是一种开源软件,可从https://github.com/guidmt/GMIEC-shiny获得。GMIEC为基因组医学提供了一个简单的界面。GMIEC与Shiny一起开发,旨在提供不需要高级编程技能的应用程序。GMIEC包括三个子应用程序,分别用于分析(GMIEC-AN),可视化(GMIEC-VIS)和结果探索(GMIEC-RES)。GMIEC是一种开源软件,可从https://github.com/guidmt/GMIEC-shiny获得。
更新日期:2020-09-10
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