7/25/2023 0 Comments Cytoscape 2.8![]() ![]() In total, 76 effective compounds were obtained using the K-nearest neighbors model, and seven botanical drugs were identified as Gao Shen Formula by hierarchical clustering. Results: A total of 14 botanical drugs and five symptom communities were obtained from real-world clinical data. Animal experiments were performed at the target and pathway levels to analyze the mechanism. The clinical efficacy of botanical drugs was verified by a retrospective cohort. Hierarchical clustering was used to screen for effective botanical drugs. The K-nearest neighbors (KNN) model was used to analyze the clinical and biological characteristics of botanical drug compounds to determine the effective compounds. Methods: In this study, based on the electronic medical record data on Hypertensive nephropathy, the core botanical drugs and patients’ symptoms were mined using the hierarchical network extraction and fast unfolding algorithm, and the protein interaction network between botanical drugs and Hypertensive nephropathy was established. ![]() The purpose of this study is to develop a prescription for improving hypertensive nephropathy, explore the evidence related to clinical application of the prescription, and verify its molecular mechanism of action. However, botanical drug prescriptions have not been summarized. Traditional Chinese medicine has long been used in the clinical treatment of Hypertensive nephropathy. 4Department of Cardiovascular, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, Chinaīackground/aim: Hypertensive nephropathy (HN) is a common complication of hypertension.3Medical Services Section, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, China.2School of Chinese Medicine, Hong Kong Baptist University, Kowloon, Hong Kong SAR,China.1School of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China. ![]() Arguably, one of the most used environments is the statistical programming language The availability of high-throughput experimental data has led to the development of multiple computational methods to analyse these data.Jia-Ming Huan 1 †, Xi-Ting Ma 2 †, Si-Yi Li 1 †, Dong-Qing Hu 3, Hao-Yu Chen 4, Yi-Min Wang 1, Xiao-Yi Su 1, Wen-Ge Su 4* and Yi-Fei Wang 4* Furthermore,īioconductor 2 provides a comprehensive collection of packages to analyse biological data developed in Multiple R packages for computational biology and bioinformatics are available in various resources such as the Comprehensive R Archive Network (CRAN). It is an open-source project hosting 671 active and curated software packages as of September 2013.įor those not familiar with computational programming, learning These packages are subject to stringent quality control in terms of functionality and documentation. ![]() R and running packages can be a time consuming task and therefore the use of intuitive graphical interfaces can enhance the usability of the tool.Ĥ is a Java open-source framework with an intuitive graphical interface devoted to the visualization and analysis of networks. Therefore, we developedĬytoscape that facilitates an interface between anyĬyrface is designed to integrate the major strengths ofĬytoscape environments by providing a general It is arguably one of the most used tools in bioinformatics, and has a variety of plug-ins to solve numerous computational biology problems. By linking these two environments,Ĭyrface allows one to use Cytoscape as a user interface for R packages andĬytoscape plug-ins in order to reach the wealth of methods implemented inĨ can call R packages from a graphical user interface (GUI)-based interface. Java open-source tool for the general development and execution of workflows. Galaxy is an open-source web-platform to assemble workflows based on genomic experimental data analysis. Thus, Cyrface complements Taverna and Galaxy by enhancing GUIs for R within a different environment with complementary features. RCytoscape is to handle experimental data from Java in the opposite direction of Cyrface: it supports the connection from It is aīioconductor R package that establishes a connection between RCytoscape 9 is another tool that exists to link R and Cytoscape. Then, to illustrate the applicability ofĬyrface, and we create a simplified version of theĭataRail 12 workflow to process and visualize experimental data using methods available in This paper is structured as follows: Firstly, we provide a description of the implementation ofĬyrface. On the one hand, to support the communication between Interaction between these two different environments (invoking ImplementationĬyrface is a Java open-source framework developed to establish the connection between Finally, we discuss on-going and future developments. ![]()
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