Search results for "shiny"
showing 6 items of 6 documents
iSEE: Interactive SummarizedExperiment Explorer
2018
Data exploration is critical to the comprehension of large biological data sets generated by high-throughput assays such as sequencing. However, most existing tools for interactive visualisation are limited to specific assays or analyses. Here, we present the iSEE (Interactive SummarizedExperiment Explorer) software package, which provides a general visual interface for exploring data in a SummarizedExperiment object. iSEE is directly compatible with many existing R/Bioconductor packages for analysing high-throughput biological data, and provides useful features such as simultaneous examination of (meta)data and analysis results, dynamic linking between plots and code tracking for reproduci…
pcaExplorer: an R/Bioconductor package for interacting with RNA-seq principal components
2019
AbstractBackgroundPrincipal component analysis (PCA) is frequently useentirely written ind in genomics applications for quality assessment and exploratory analysis in high-dimensional data, such as RNA sequencing (RNA-seq) gene expression assays. Despite the availability of many software packages developed for this purpose, an interactive and comprehensive interface for performing these operations is lacking.ResultsWe developed the pcaExplorer software package to enhance commonly performed analysis steps with an interactive and user-friendly application, which provides state saving as well as the automated creation of reproducible reports. pcaExplorer is implemented in R using the Shiny fra…
ideal: an R/Bioconductor package for interactive differential expression analysis
2020
AbstractBackgroundRNA sequencing (RNA-seq) is an ever increasingly popular tool for transcriptome profiling. A key point to make the best use of the available data is to provide software tools that are easy to use but still provide flexibility and transparency in the adopted methods. Despite the availability of many packages focused on detecting differential expression, a method to streamline this type of bioinformatics analysis in a comprehensive, accessible, and reproducible way is lacking.ResultsWe developed the ideal software package, which serves as a web application for interactive and reproducible RNA-seq analysis, while producing a wealth of visualizations to facilitate data interpr…
GeneTonic: an R/Bioconductor package for streamlining the interpretation of RNA-seq data
2021
AbstractBackgroundThe interpretation of results from transcriptome profiling experiments via RNA sequencing (RNA-seq) can be a complex task, where the essential information is distributed among different tabular and list formats - normalized expression values, results from differential expression analysis, and results from functional enrichment analyses. A number of tools and databases are widely used for the purpose of identification of relevant functional patterns, yet often their contextualization within the data and results at hand is not straightforward, especially if these analytic components are not combined together efficiently.ResultsWe developed the GeneTonic software package, whi…
deaR-Shiny: An Interactive Web App for Data Envelopment Analysis
2021
In this paper, we describe an interactive web application (deaR-shiny) to measure efficiency and productivity using data envelopment analysis (DEA). deaR-shiny aims to fill the gap that currently exists in the availability of online DEA software offering practitioners and researchers free access to a very wide variety of DEA models (both conventional and fuzzy models). We illustrate how to use the web app by replicating the main results obtained by Carlucci, Cirà and Coccorese in 2018, who investigate the efficiency and economic sustainability of Italian regional airport by using two conventional DEA models, and the results given by Kao and Liu in their papers published in 2000 and 2003, wh…
Utility of Alternative Effect Size Statistics and the Development of a Web-Based Calculator: Shiny-AESC
2018
Alternative displays of effect size statistics can enhance the understandability and impact of validity evidence in a variety of applied settings. Arguably, the proliferation of alternative effect size statistics has been limited due to the lack of user-friendly tools to create them. Common statistical packages do not readily produce these alternative effect sizes and existing tools are outdated and inaccessible. In this paper, I introduce a free-to-use web-based calculator (https://dczhang.shinyapps.io/expectancyApp/) for generating alternative effect size displays from empirical data. This calculator requires no mathematical or programming expertise, and therefore, is ideal for academics …