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Journal articles on the topic 'Application Shiny'

Author: Grafiati

Published: 26 October 2024

Last updated: 31 July 2025

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1

Shirokovskikh, Margarita S. "THE APPLICATION OF SHINY MATERIALS IN TAPESTRY: FROM DECOR TO CONCEPT." Architecton: Proceedings of Higher Education, no. 2(70) (June 29, 2020): 21. http://dx.doi.org/10.47055/1990-4126-2020-2(70)-21.

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This article is the first ever attempt to study and summarize the extensive material on the use of shiny threads in tapestry art. The circle of artists using shine as an expressive medium in their artworks is identified. Methods of creating shiny surfaces in this art form and their symbolic meanings are outlined.

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Morota, Gota. "79 Statistical Graphics and Interactive Visualization in Animal Science." Journal of Animal Science 99, Supplement_3 (2021): 45. http://dx.doi.org/10.1093/jas/skab235.079.

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Abstract Statistical graphics has advanced significantly in recent years with the development of statistical computing tools that allow us to create reports dynamically, facilitate reproducible research, and explore data interactively. In particular, data visualization is a fundamental aspect of big data analysis in animal science. However, the static nature of standard visualization limits the information that can be displayed and extracted. The objectives of this hands-on workshop are to learn how to utilize interactive visualization and investigate both global and local structures of graphs

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Morota, Gota. "312 Statistical graphics and interactive visualization in animal science." Journal of Animal Science 98, Supplement_4 (2020): 45–46. http://dx.doi.org/10.1093/jas/skaa278.083.

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Abstract Statistical graphics has advanced significantly in recent years with the development of statistical computing tools that allow us to create reports dynamically, facilitate reproducible research, and explore data interactively. In particular, data visualization is a fundamental aspect of big data analysis in animal science. However, the static nature of standard visualization limits the information that can be displayed and extracted. The objectives of this hands-on workshop are to learn how to utilize interactive visualization and investigate both global and local structures of graphs

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Jagla, Bernd, Valentina Libri, Claudia Chica, et al. "SCHNAPPs - Single Cell sHiNy APPlication(s)." Journal of Immunological Methods 499 (December 2021): 113176. http://dx.doi.org/10.1016/j.jim.2021.113176.

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Chaves, Marcelo Vitor Gualberto Santos, Marcelo Lourençoni Pauletti, Samuel José Silva Soares da Rocha, Lucas Rezende Gomide, and Carolina Souza Jarochinski e. Silva. "Edentree: A web application for optimal rotation age analysis." Revista Árvore 49, no. 1 (2025): 1–18. https://doi.org/10.53661/1806-9088202549263865.

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The R/Shiny package is a tool that allows the creation of interactive web applications, transforming complex analyses into accessible interfaces. In the forestry sector, Shiny’s potential is still little explored, despite its applications in areas such as forest inventory, fire monitoring, LiDAR data analysis, and biomass and carbon estimates in Brazilian forests. This tool has been adopted by researchers and companies for its ability to generate interactive statistical reports and dashboards, contributing to data visualization and supporting forestry decision-making. From this, the objective

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Kemperman, Lauren, and Matthew N. McCall. "miRcomp-Shiny: Interactive assessment of qPCR-based microRNA quantification and quality control algorithms." F1000Research 6 (November 23, 2017): 2046. http://dx.doi.org/10.12688/f1000research.13098.1.

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The miRcomp-Shiny web application allows interactive performance assessments and comparisons of qPCR-based microRNA expression and quality estimation methods using a benchmark data set. This work is motivated by two distinct use cases: (1) selection of methodology and quality thresholds for use analyzing one's own data, and (2) comparison of novel expression estimation algorithms with currently-available methodology. The miRcomp-Shiny application is implemented in the R/Shiny language and can be installed on any operating system on which R can be installed. It is made freely available as part

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Li, Jianfeng, Bowen Cui, Yuting Dai, Ling Bai, and Jinyan Huang. "BioInstaller: a comprehensive R package to construct interactive and reproducible biological data analysis applications based on the R platform." PeerJ 6 (October 31, 2018): e5853. http://dx.doi.org/10.7717/peerj.5853.

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The increase in bioinformatics resources such as tools/scripts and databases poses a great challenge for users seeking to construct interactive and reproducible biological data analysis applications. Here, we propose an open-source, comprehensive, flexible R package named BioInstaller that consists of the R functions, Shiny application, the HTTP representational state transfer application programming interfaces, and a docker image. BioInstaller can be used to collect, manage and share various types of bioinformatics resources and perform interactive and reproducible data analyses based on the

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Oberti, Mauricio, and Iosif Vaisman. "shiny-pred: a server for the prediction of protein disordered regions." F1000Research 8 (February 28, 2019): 230. http://dx.doi.org/10.12688/f1000research.17669.1.

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Intrinsically disordered proteins or intrinsically disordered regions (IDR) are segments within a protein chain lacking a stable three-dimensional structure under normal physiological conditions. Accurate prediction of IDRs is challenging due to their genome wide occurrence and low ratio of disordered residues, making them a difficult target for traditional classification techniques. Existing computational methods mostly rely on sequence profiles to improve accuracy, which is time consuming and computationally expensive. The shiny-pred application is an ab initio sequence-only disorder predict

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Sağlam, Fatih``, Tuba Şanlı, and Mehmet Ali Cengiz. "ShinySurv : A survival analysis and Shiny web application." Journal of Statistics and Management Systems 27, no. 8 (2024): 1557–75. https://doi.org/10.47974/jsms-1024.

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There are different programs available for survival analysis. However, these programs do not deal with survival problems with all censor types. The aim of this study is to form and explain “ShinySurv” application of survival analysis methods in R-Shiny for different types of censorship. Using ShinySurv, the user can upload his own data set to the system or benefit from sample data sets. ShinySurv provides visualization of analysis results with graphs and reporting of results for parametric and non-parametric survival methods. An example application of a survival analysis is given. The web appl

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Toledo San Martín, Álvaro, and Inés Vicencio Pardo. "Aplicaciones interactivas basadas en el paquete SHINY/R para explicar conceptos estadísticos." HUMAN REVIEW. International Humanities Review / Revista Internacional De Humanidades 17, no. 4 (2023): 1–15. https://doi.org/10.37819/revhuman.v17i4.1587.

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Shiny is an application for R software that allows the creation of interfaces for users without programming knowledge. In this work we use a systematic mapping method for the collection, analysis, and extraction of information in publications that indicate the use of Shiny to explain statistical concepts. Among the conclusions, it is found that Shiny is used as a tool for carrying out academic experiences, as well as a means for solving problems in the areas of education and natural and life sciences, addressing statistical topics related to pre-inferential statistics and inferential statistic

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Bernardo, Nicholas D., and Gretchen A. Macht. "Learning ‘Learning Curves’ with R Shiny." Proceedings of the Human Factors and Ergonomics Society Annual Meeting 65, no. 1 (2021): 1567–71. http://dx.doi.org/10.1177/1071181321651119.

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Learning curves are fundamental in understanding individual task performance, with ubiquitous implementation in task assignments, worker scheduling, team formulation, etc., in domains bridging from manufacturing to healthcare. With a broad range of applicability, it is critical that students conceptualize, visualize, and build learning curves to activate that knowledge for effective decision-making. This paper describes a hands-on experiential approach for teaching learning curves that utilizes building LEGO® sets with mathematical formulation and data visualization in an open-source R Shiny a

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Marusich, Laura R., and Jonathan Z. Bakdash. "rmcorrShiny: A web and standalone application for repeated measures correlation." F1000Research 10 (November 8, 2021): 697. http://dx.doi.org/10.12688/f1000research.55027.2.

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We describe a web and standalone Shiny app for calculating the common, linear within-individual association for repeated assessments of paired measures with multiple individuals: repeated measures correlation (rmcorr). This tool makes rmcorr more widely accessible, providing a graphical interface for performing and visualizing the output of analysis with rmcorr. In contrast to rmcorr, most widely used correlation techniques assume paired data are independent. Incorrectly analyzing repeated measures data as independent will likely produce misleading results. Using aggregation or separate models

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Marusich, Laura R., and Jonathan Z. Bakdash. "rmcorrShiny: A web and standalone application for repeated measures correlation." F1000Research 10 (July 30, 2021): 697. http://dx.doi.org/10.12688/f1000research.55027.1.

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We describe a web and standalone Shiny app for calculating the common, linear within-individual association for repeated assessments of paired measures with multiple individuals: repeated measures correlation (rmcorr). This tool makes rmcorr more widely accessible, providing a graphical interface for performing and visualizing the output of analysis with rmcorr. In contrast to rmcorr, most widely used correlation techniques assume paired data are independent. Incorrectly analyzing repeated measures data as independent will likely produce misleading results. Using aggregation or separate models

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Germani, Elodie, Hugues Lelouard, and Mathieu Fallet. "SAPHIR: a Shiny application to analyze tissue section images." F1000Research 9 (April 8, 2021): 1276. http://dx.doi.org/10.12688/f1000research.27062.2.

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Study of cell populations in tissues using immunofluorescence is a powerful method for both basic and medical research. Image acquisitions performed by confocal microscopy notably allow excellent lateral resolution and more than 10 parameter measurements when using spectral or multiplex imaging. Analysis of such complex images can be very challenging and easily lead to bias and misinterpretation. Here, we have developed the Shiny Analytical Plot of Histological Image Results (SAPHIR), an R shiny application for histo-cytometry using scatterplot representation of data extracted by segmentation.

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Germani, Elodie, Hugues Lelouard, and Mathieu Fallet. "SAPHIR: a Shiny application to analyze tissue section images." F1000Research 9 (October 27, 2020): 1276. http://dx.doi.org/10.12688/f1000research.27062.1.

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Study of cell populations in tissues using immunofluorescence is a powerful method for both basic and medical research. Image acquisitions performed by confocal microscopy notably allow excellent lateral resolution and more than 10 parameter measurement when using spectral or multiplex imaging. Analysis of such complex images can be very challenging and easily lead to bias and misinterpretation. Here, we have developed the Shiny Analytical Plot of Histological Image Results (SAPHIR), an R shiny application for histo-cytometry using scatterplot representation of data extracted by segmentation.

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Oktavia, Cintika, Budi Warsito, and Vincensius Gunawan Slamet Kadarrisman. "Development of Customer Loyalty Measurement Application using R Shiny." E3S Web of Conferences 448 (2023): 02038. http://dx.doi.org/10.1051/e3sconf/202344802038.

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Shopee is a successful e-commerce platform in Southeast Asia today, becoming the leading choice for customers who want to shop online and has built loyal relationships with customers. Apart from Shopee, many other e-commerce companies also emphasize the importance of building customer loyalty as their primary goal. This research will explore the main factors that play a role in creating Shopee customer loyalty. By measuring customer loyalty, which refers to the variables of customer satisfaction, promotions, data security, and customer service. Through the Structural Equation Modeling Partial

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Uttiramerur, Arvind. "Streamlining Clinical Trial Data from Raw to Regulatory Submission with R Shiny and Pharmaverse." INTERANTIONAL JOURNAL OF SCIENTIFIC RESEARCH IN ENGINEERING AND MANAGEMENT 08, no. 10 (2024): 1–15. http://dx.doi.org/10.55041/ijsrem36907.

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In recent years, the pharmaceutical and biotech industries have increasingly adopted open-source tools to enhance the efficiency, transparency, and reproducibility of clinical trial data analysis. R Shiny, a web application framework for R, has become a key component in creating interactive dashboards and visualizations that support real-time data exploration and decision-making. As part of the Pharmaverse ecosystem, R Shiny plays a vital role in regulatory submissions, data analysis, and reporting, offering dynamic, user-friendly interfaces for clinical trial monitoring, patient safety report

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Johnson, Olatunji, Claudio Fronterre, Peter J. Diggle, Benjamin Amoah, and Emanuele Giorgi. "MBGapp: A Shiny application for teaching model-based geostatistics to population health scientists." PLOS ONE 16, no. 12 (2021): e0262145. http://dx.doi.org/10.1371/journal.pone.0262145.

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User-friendly interfaces have been increasingly used to facilitate the learning of advanced statistical methodology, especially for students with only minimal statistical training. In this paper, we illustrate the use of MBGapp for teaching geostatistical analysis to population health scientists. Using a case-study on Loa loa infections, we show how MBGapp can be used to teach the different stages of a geostatistical analysis in a more interactive fashion. For wider accessibility and usability, MBGapp is available as an R package and as a Shiny web-application that can be freely accessed on an

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Gu, Zuguang, and Daniel Hübschmann. "Make Interactive Complex Heatmaps in R." Bioinformatics 38, no. 5 (2021): 1460–62. http://dx.doi.org/10.1093/bioinformatics/btab806.

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Abstract Summary Heatmap is a powerful visualization method on two-dimensional data to reveal patterns shared by subsets of rows and columns. In this work, we introduce a new R package InteractiveComplexHeatmap that brings interactivity to the widely used ComplexHeatmap package. InteractiveComplexHeatmap is designed with an easy-to-use interface where static complex heatmaps can be directly exported to an interactive Shiny web application only with one additional line of code. InteractiveComplexHeatmap also provides flexible functionalities for integrating interactive heatmap widgets to build

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Rudenok, V. A., O. M. Kanunnikova, G. N. Aristova, and O. S. Tikhonova. "The design and properties of galvanic anticorrosive coatings for important precision parts of farming equipment." IOP Conference Series: Earth and Environmental Science 949, no. 1 (2022): 012113. http://dx.doi.org/10.1088/1755-1315/949/1/012113.

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Abstract The paper explores the possibility of using a number of nickel alloys in multilayer coatings to decrease nickel consumption and preserve the functional effect of the coating. The following is proved by the graphical calculation technique using experimental data on the galvanic properties of the multilayer coating parts. Nickel-iron, nickel-phosphorus and nickel-tin alloy can be applied as a lower coating layer rather than semi-shiny, shiny or composite nickel. It is advisable to use a nickel-iron alloy as the middle (second) layer, and the concentration of iron depends on the composit

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Siqueira, Daniel, Gabriel Rodrigues da Silva, Luan Patrick Moura de Souza, Carlos Antônio Zarzar, and Paulo Roberto Brasil Santos. "Developing a Robust Shiny Application Integrated with SQL Databases for Aquaculture." Sigmae 13, no. 4 (2024): 253–64. https://doi.org/10.29327/2520355.13.4-24.

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Este trabalho apresenta o desenvolvimento de uma aplicação para gerenciamento de compras coletivas de ração na aquicultura, visando redução de custos e otimização logística. Tem como objetivo validar a robustez de aplicações desenvolvidas utilizando o framework Shiny da linguagem de programação R por meio da integração de um Sistema de Gerenciamento de Banco de Dados (SGBD) no backend, visando desmistificar a percepção predominante de que o Shiny é exclusivamente uma ferramenta de prototipação, demonstrando sua viabilidade para aplicações robustas de produção. A metodologia adotada abrange trê

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Danger, Richard, Quentin Moiteaux, Yodit Feseha, Estelle Geffard, Gérard Ramstein, and Sophie Brouard. "FaDA: A web application for regular laboratory data analyses." PLOS ONE 16, no. 12 (2021): e0261083. http://dx.doi.org/10.1371/journal.pone.0261083.

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Web-based data analysis and visualization tools are mostly designed for specific purposes, such as the analysis of data from whole transcriptome RNA sequencing or single-cell RNA sequencing. However, generic tools designed for the analysis of common laboratory data for noncomputational scientists are also needed. The importance of such web-based tools is emphasized by the continuing increases in the sample capacity of conventional laboratory tools such as quantitative PCR, flow cytometry or ELISA instruments. We present a web-based application FaDA, developed with the R Shiny package that prov

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Class, Caleb A., Min Jin Ha, Veerabhadran Baladandayuthapani, and Kim-Anh Do. "iDINGO—integrative differential network analysis in genomics with Shiny application." Bioinformatics 34, no. 7 (2017): 1243–45. http://dx.doi.org/10.1093/bioinformatics/btx750.

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Rigby, James, and Zach Traylor. "Capturing Trends in Industrial-Organizational Psychology: A Shiny Web Application." Human Performance 33, no. 4 (2020): 302–6. http://dx.doi.org/10.1080/08959285.2020.1751165.

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Yu, Chi-Lin, and Ching-Fan Sheu. "EFAshiny: An User-Friendly Shiny Application for Exploratory Factor Analysis." Journal of Open Source Software 3, no. 22 (2018): 567. http://dx.doi.org/10.21105/joss.00567.

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Okour, Malek. "DosePredict: A Shiny Application for Generalized Pharmacokinetics‐Based Dose Predictions." Journal of Clinical Pharmacology 60, no. 11 (2020): 1502–8. http://dx.doi.org/10.1002/jcph.1649.

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Uttiramerur, Arvind. "Managing Adverse Events in Clinical Trials with R and Shiny." INTERANTIONAL JOURNAL OF SCIENTIFIC RESEARCH IN ENGINEERING AND MANAGEMENT 08, no. 10 (2024): 1–15. http://dx.doi.org/10.55041/ijsrem36769.

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Adverse events (AEs) are critical occurrences that can significantly impact patient safety and the overall success of clinical trials. Effective management of AEs is essential for ensuring regulatory compliance and safeguarding participants' well-being. This paper explores the integration of R and Shiny as innovative tools for the real-time monitoring, visualization, and analysis of AEs in clinical trials. By leveraging R’s robust statistical capabilities and Shiny’s interactive interface, researchers can enhance data management processes, facilitate informed decision- making, and foster colla

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Hassan Ali, Ahmed, Michelle Flood, Ciara Kirke, et al. "RxTrends: An R-based Shiny Application for Visualising Open Data on Prescribed Medications in Ireland." HRB Open Research 8 (May 27, 2025): 36. https://doi.org/10.12688/hrbopenres.14080.2.

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Background The Health Service Executive (HSE) in Ireland releases monthly reports on prescription dispensing claims and payments relating to community drug schemes. This paper describes the implementation of an R-based Shiny application that facilitates interactive visualisation and analysis of trends in medication prescribing and improves the data’s practical value, and presents use cases focused on drug utilisation and medication policy questions. Methods Using Primary Care Reimbursement Service (PCRS) data provided by the HSE relating to the means-tested General Medical Services (GMS) schem

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Hassan Ali, Ahmed, Michelle Flood, Ciara Kirke, et al. "RxTrends: An R-based Shiny Application for Visualising Open Data on Prescribed Medications in Ireland." HRB Open Research 8 (February 26, 2025): 36. https://doi.org/10.12688/hrbopenres.14080.1.

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Background The Health Service Executive (HSE) in Ireland releases monthly reports on prescription dispensing claims and payments relating to community drug schemes. This paper describes the implementation of an R-based Shiny application that facilitates user-friendly visualisation and analysis of trends in medication prescribing and improves the data’s practical value, and presents use cases focused on drug utilisation and medication policy questions. Methods Using Primary Care Reimbursement Service (PCRS) data provided by the HSE relating to the means-tested General Medical Services (GMS) sch

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Zhang, Xiao-Fei, Le Ou-Yang, Shuo Yang, Xing-Ming Zhao, Xiaohua Hu, and Hong Yan. "EnImpute: imputing dropout events in single-cell RNA-sequencing data via ensemble learning." Bioinformatics 35, no. 22 (2019): 4827–29. http://dx.doi.org/10.1093/bioinformatics/btz435.

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Abstract Summary Imputation of dropout events that may mislead downstream analyses is a key step in analyzing single-cell RNA-sequencing (scRNA-seq) data. We develop EnImpute, an R package that introduces an ensemble learning method for imputing dropout events in scRNA-seq data. EnImpute combines the results obtained from multiple imputation methods to generate a more accurate result. A Shiny application is developed to provide easier implementation and visualization. Experiment results show that EnImpute outperforms the individual state-of-the-art methods in almost all situations. EnImpute is

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Aswi, Aswi, Muhammad Arif Tiro, Sudarmin Sudarmin, et al. "MAKING BAYESIAN DISEASE MAPPING EASY AND INTERACTIVE: AN R SHINY APPLICATION." MEDIA STATISTIKA 16, no. 2 (2023): 148–59. http://dx.doi.org/10.14710/medstat.16.2.148-159.

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Spatial analysis of count data is important in epidemiology and other domains to identify spatial patterns. While Bayesian spatial models are a popular approach, they do require detailed knowledge of the process for model fitting, checking, and visualising results. Although a number of R packages are available to simplify running the model, there are still complexities when checking the model. This paper aims to provide a user-friendly and interactive R Shiny web application for the analysis of spatial data using Bayesian spatial Conditional Autoregressive Leroux models. The web application is

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Obermayer, Alyssa, Li Dong, Qianqian Hu, et al. "DRPPM-EASY: A Web-Based Framework for Integrative Analysis of Multi-Omics Cancer Datasets." Biology 11, no. 2 (2022): 260. http://dx.doi.org/10.3390/biology11020260.

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High-throughput transcriptomic and proteomic analyses are now routinely applied to study cancer biology. However, complex omics integration remains challenging and often time-consuming. Here, we developed DRPPM-EASY, an R Shiny framework for integrative multi-omics analysis. We applied our application to analyze RNA-seq data generated from a USP7 knockdown in T-cell acute lymphoblastic leukemia (T-ALL) cell line, which identified upregulated expression of a TAL1-associated proliferative signature in T-cell acute lymphoblastic leukemia cell lines. Next, we performed proteomic profiling of the U

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Nurul, Syakima Ab Mutalib. "EpigenomeViewer: A Shiny Web Application for Visualizing Methylation Patterns Across Biological Samples." Malaysia Journal of Invention and Innovation 4, no. 2 (2025): 34–42. https://doi.org/10.5281/zenodo.14822076.

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DNA methylation plays a crucial role in gene regulation and is involved in the development of numerous diseases including cancer. However, researchers often face challenges in visualising and analysing methylation data because of limited accessibility to user-friendly software that integrates interactive visualisation with bioinformatics analysis. EpigenomeViewer is a Shiny web application developed to address this gap by providing a comprehensive platform for visualising DNA methylation patterns across tumour and normal biological samples. Users can upload their differentially methylated prob

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Nurul Syakima Ab Mutalib. "EpigenomeViewer: A Shiny Web Application for Visualizing Methylation Patterns Across Biological Samples." Malaysia Journal of Invention and Innovation 4, no. 2 (2025): 34–42. https://doi.org/10.64382/mjii.v4i2.83.

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DNA methylation plays a crucial role in gene regulation and is involved in the development of numerous diseases including cancer. However, researchers often face challenges in visualising and analysing methylation data because of limited accessibility to user-friendly software that integrates interactive visualisation with bioinformatics analysis. EpigenomeViewer is a Shiny web application developed to address this gap by providing a comprehensive platform for visualising DNA methylation patterns across tumour and normal biological samples. Users can upload their differentially methylated prob

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Gaythorpe, Katy, Aaron Morris, Natsuko Imai, Miles Stewart, Jeffrey Freeman, and Mary Choi. "Chainchecker: An application to visualise and explore transmission chains for Ebola virus disease." PLOS ONE 16, no. 2 (2021): e0247002. http://dx.doi.org/10.1371/journal.pone.0247002.

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2020 saw the continuation of the second largest outbreak of Ebola virus disease (EVD) in history. Determining epidemiological links between cases is a key part of outbreak control. However, due to the large quantity of data and subsequent data entry errors, inconsistencies in potential epidemiological links are difficult to identify. We present chainchecker, an online and offline shiny application which visualises, curates and verifies transmission chain data. The application includes the calculation of exposure windows for individual cases of EVD based on user defined incubation periods and u

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Lacroix, Laurent. "G4HunterApps." Bioinformatics 35, no. 13 (2018): 2311–12. http://dx.doi.org/10.1093/bioinformatics/bty951.

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Abstract Motivation In order to help G4Hunter users and make it more accessible, I have developed a set of small applications within the Shiny/R framework. Results Each application fulfils simple tasks ranging from computing the G4Hunter score for a sequence or a list of sequence to extracting sequences with a G4Hunter score above a threshold for a sequence up to 5 Mb or a list of short sequences. The application can be installed either on the user computer within Rstudio or on a Rstudio server. Availability and implementation The source code for the ShinyApps is available on GitHub (https://g

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Sakhteman, Amirhossein, Arindam Ghosh, and Vittorio Fortino. "EDTox: an R Shiny application to predict the endocrine disruption potential of compounds." Bioinformatics 38, no. 7 (2022): 2066–69. http://dx.doi.org/10.1093/bioinformatics/btac045.

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Abstract Purpose Endocrine disruptors are a rising concern due to the wide array of health issues that it can cause. Although there are tools for mode of action (MoA)-based prediction of endocrine disruption (e.g. QSAR Toolbox and iSafeRat), none of them is based on toxicogenomics data. Here, we present EDTox, an R Shiny application enabling users to explore and use a computational method that we have recently published to identify and prioritize endocrine disrupting (ED) chemicals based on toxicogenomic data. The EDTox pipeline utilizes previously trained toxicogenomic-driven classifiers to m

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Terzi di Bergamo, Lodovico, Francesca Guidetti, Davide Rossi, Francesco Bertoni, and Luciano Cascione. "HTGQC and shinyHTGQC: an R package and shinyR application for quality controls of HTG EDGE-seq protocols." Gigabyte 2022 (December 2, 2022): 1–5. http://dx.doi.org/10.46471/gigabyte.74.

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Extraction-free HTG EdgeSeq protocols are used to profile sets of genes and measure their expression. Thus, these protocols are frequently used to characterise tumours and their microenvironments. However, although positive and control genes are provided, little indication is given concerning the assessment of the technical success of each sample within the sequencing run. We developed HTGQC, an R package for the quality control of HTG EdgeSeq protocols. Additionally, shinyHTGQC is a shiny application for users without computing knowledge, providing an easy-to-use interface for data quality co

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Andersen, Nico, and Fabian Zehner. "shinyReCoR: A Shiny Application for Automatically Coding Text Responses Using R." Psych 3, no. 3 (2021): 422–46. http://dx.doi.org/10.3390/psych3030030.

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In this paper, we introduce shinyReCoR: a new app that utilizes a cluster-based method for automatically coding open-ended text responses. Reliable coding of text responses from educational or psychological assessments requires substantial organizational and human effort. The coding of natural language in responses to tests depends on the texts’ complexity, corresponding coding guides, and the guides’ quality. Manual coding is thus not only expensive but also error-prone. With shinyReCoR, we provide a more efficient alternative. The use of natural language processing makes texts utilizable for

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Lakshmanan, Karthick, Arul Prakasham Peter, Shylajanaciyar Mohandass, Sangeetha Varadharaj, Uma Lakshmanan, and Prabaharan Dharmar. "SynRio: R and Shiny based application platform for cyanobacterial genome analysis." Bioinformation 11, no. 9 (2015): 422–25. http://dx.doi.org/10.6026/97320630011422.

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Jiang, Youxiang, Qing Zeng, and Hongbo Wen. "TestAnaAPP: An interactive R-shiny application for various test analysis methods." SoftwareX 28 (December 2024): 101967. http://dx.doi.org/10.1016/j.softx.2024.101967.

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Yu, Yiming, Yidan Ouyang, and Wen Yao. "shinyCircos: an R/Shiny application for interactive creation of Circos plot." Bioinformatics 34, no. 7 (2017): 1229–31. http://dx.doi.org/10.1093/bioinformatics/btx763.

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McMurdie, P. J., and S. Holmes. "Shiny-phyloseq: Web application for interactive microbiome analysis with provenance tracking." Bioinformatics 31, no. 2 (2014): 282–83. http://dx.doi.org/10.1093/bioinformatics/btu616.

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Jagadesan, Sankarasubramanian, and Chittibabu Guda. "MetaDAVis: An R shiny application for metagenomic data analysis and visualization." PLOS ONE 20, no. 4 (2025): e0319949. https://doi.org/10.1371/journal.pone.0319949.

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The human microbiome exerts tremendous influence on maintaining a balance between human health and disease. High-throughput sequencing has enabled the study of microbial communities at an unprecedented resolution. Generation of massive amounts of sequencing data has also presented novel challenges to analyzing and visualizing data to make biologically relevant interpretations. We have developed an interactive Metagenome Data Analysis and Visualization (MetaDAVis) tool for 16S rRNA as well as the whole genome sequencing data analysis and visualization to address these challenges using an R Shin

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Nieuwenhuijse, David F., Bas B. Oude Munnink, and Marion P. G. Koopmans. "viromeBrowser: A Shiny App for Browsing Virome Sequencing Analysis Results." Viruses 13, no. 3 (2021): 437. http://dx.doi.org/10.3390/v13030437.

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Experiments in which complex virome sequencing data is generated remain difficult to explore and unpack for scientists without a background in data science. The processing of raw sequencing data by high throughput sequencing workflows usually results in contigs in FASTA format coupled to an annotation file linking the contigs to a reference sequence or taxonomic identifier. The next step is to compare the virome of different samples based on the metadata of the experimental setup and extract sequences of interest that can be used in subsequent analyses. The viromeBrowser is an application writ

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Contrino, Bruno, Eric Miele, Ronald Tomlinson, M. Paola Castaldi, and Piero Ricchiuto. "DOSCHEDA: a web application for interactive chemoproteomics data analysis." PeerJ Computer Science 3 (August 28, 2017): e129. http://dx.doi.org/10.7717/peerj-cs.129.

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Background Mass Spectrometry (MS) based chemoproteomics has recently become a main tool to identify and quantify cellular target protein interactions with ligands/drugs in drug discovery. The complexity associated with these new types of data requires scientists with a limited computational background to perform systematic data quality controls as well as to visualize the results derived from the analysis to enable rapid decision making. To date, there are no readily accessible platforms specifically designed for chemoproteomics data analysis. Results We developed a Shiny-based web application

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Messori, Andrea, Vera Damuzzo, Melania Rivano, et al. "Application of the IPDfromKM-Shiny Method to Compare the Efficacy of Novel Treatments Aimed at the Same Disease Condition: A Report of 14 Analyses." Cancers 15, no. 6 (2023): 1633. http://dx.doi.org/10.3390/cancers15061633.

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In the area of evidence-based medicine, the IPDfromKM-Shiny method is an innovative method of survival analysis, midway between artificial intelligence and advanced statistics. Its main characteristic is that an original software investigates the Kaplan-Meier graphs of trials so that individual-patient data are reconstructed. These reconstructed patients represent a new form of original clinical material. The typical objective of investigations based on this method is to analyze the available evidence, especially in oncology, to perform indirect comparisons, and determine the place in therapy

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Savini, Lara, Luca Candeloro, Samuel Perticara, and Annamaria Conte. "EpiExploreR: A Shiny Web Application for the Analysis of Animal Disease Data." Microorganisms 7, no. 12 (2019): 680. http://dx.doi.org/10.3390/microorganisms7120680.

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Emerging and re-emerging infectious diseases are a significant public and animal health threat. In some zoonosis, the early detection of virus spread in animals is a crucial early warning for humans. The analyses of animal surveillance data are therefore of paramount importance for public health authorities to identify the appropriate control measure and intervention strategies in case of epidemics. The interaction among host, vectors, pathogen and environment require the analysis of more complex and diverse data coming from different sources. There is a wide range of spatiotemporal methods th

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Smith, Robert, and Paul Schneider. "Making health economic models Shiny: A tutorial." Wellcome Open Research 5 (April 14, 2020): 69. http://dx.doi.org/10.12688/wellcomeopenres.15807.1.

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Health economic evaluation models have traditionally been built in Microsoft Excel, but more sophisticated tools are increasingly being used as model complexity and computational requirements increase. Of all the programming languages, R is most popular amongst health economists because it has a plethora of user created packages and is highly flexible. However, even with an integrated development environment such as R Studio, R lacks a simple point and click user interface and therefore requires some programming ability. This might make the switch from Microsoft Excel to R seem daunting, and i

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Smith, Robert, and Paul Schneider. "Making health economic models Shiny: A tutorial." Wellcome Open Research 5 (July 31, 2020): 69. http://dx.doi.org/10.12688/wellcomeopenres.15807.2.

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Health economic evaluation models have traditionally been built in Microsoft Excel, but more sophisticated tools are increasingly being used as model complexity and computational requirements increase. Of all the programming languages, R is most popular amongst health economists because it has a plethora of user created packages and is highly flexible. However, even with an integrated development environment such as R Studio, R lacks a simple point and click user interface and therefore requires some programming ability. This might make the switch from Microsoft Excel to R seem daunting, and i

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