KnowSeq R-Bioc package: The automatic smart gene expression tool for retrieving relevant biological knowledge
KnowSeq R-Bioc package: The automatic smart gene expression tool for retrieving relevant biological knowledge
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DOI：
10.1016/j.compbiomed.2021.104387
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发表时间：
2021-04-19
影响因子：
7.7
通讯作者：
Rojas, Ignacio
中科院分区：
文献类型：
--
作者：
Castillo-Secilla, Daniel;Galvez, Juan Manuel G.;Rojas, Ignacio
KnowSeq R/Bioc软件包是一款功能强大、可扩展和模块化的软件，专注于自动化和组装具有新特性和功能的知名生物信息学工具。它包括一个统一的环境来执行复杂的基因表达分析，涵盖了识别特定疾病的基因特征所需的所有处理步骤，以收集可理解的知识。该过程可以从已知平台上可用的或由用户自己提供的原始文件启动，并且在任一情况下来自不同的信息源和不同的转录组学技术。该管道利用了一套先进的算法，包括适应一个新的程序选择最具代表性的基因在一个给定的多类问题。类似地，嵌入了能够对新患者进行分类的智能系统，为用户提供了在生物信息学中许多众所周知的和广泛的分类和特征选择方法中选择一种的机会。此外，KnowSeq被设计为自动开发整个过程的完整和详细的HTML报告，该报告也是模块化和可扩展的。研究了两类乳腺癌和多类肺癌研究病例，以严格评估KnowSeq的可用性和有效性。利用这两个实验中获得的差异表达基因构建的模型达到了很高的分类率。此外，生物学知识提取基因本体，通路和相关疾病的目的是帮助专家在决策过程中。KnowSeq可在Bioconductor（https：//bioconductor.org/packages/KnowSeq）、GitHub（https：//github.com/CasedUgr/KnowSeq）和Docker（https：//hub.docker.com/r/casedugr/knowseq）上获得。
KnowSeq R/Bioc package is designed as a powerful, scalable and modular software focused on automatizing and assembling renowned bioinformatic tools with new features and functionalities. It comprises a unified environment to perform complex gene expression analyses, covering all the needed processing steps to identify a gene signature for a specific disease to gather understandable knowledge. This process may be initiated from raw files either available at well-known platforms or provided by the users themselves, and in either case coming from different information sources and different Transcriptomic technologies. The pipeline makes use of a set of advanced algorithms, including the adaptation of a novel procedure for the selection of the most representative genes in a given multiclass problem. Similarly, an intelligent system able to classify new patients, providing the user the opportunity to choose one among a number of well-known and widespread classification and feature selection methods in Bioinformatics, is embedded. Furthermore, KnowSeq is engineered to automatically develop a complete and detailed HTML report of the whole process which is also modular and scalable. Biclass breast cancer and multiclass lung cancer study cases were addressed to rigorously assess the usability and efficiency of KnowSeq. The models built by using the Differential Expressed Genes achieved from both experiments reach high classification rates. Furthermore, biological knowledge was extracted in terms of Gene Ontologies, Pathways and related diseases with the aim of helping the expert in the decision-making process. KnowSeq is available at Bioconductor (https://bioconductor.org/packages/KnowSeq), GitHub (https://github.com/CasedUgr/KnowSeq) and Docker (https://hub.docker.com/r/casedugr/knowseq).