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22 results for “R Shiny”
Extended data tables to Haering and Habermann, F1000Res, RNfuzzyApp: an R shiny RNA-seq data analysis app for visualisation, differential expression analysis, time-series clustering and enrichment analysis
<p><b>Background</b> </p> <p>RNA-seq is a widely adopted affordable method for large scale gene expression profiling. However, user-friendly and versatile tools for wet-lab biologists to analyse RNA-seq data beyond standard analyses such as differential expression, are rare. Especially, the analysis of time-series data is difficult for wet-lab biologists lacking advanced computational training. Furthermore, most meta-analysis tools are tailored for model organisms and not easily adaptable to other species.</p> <p><b>Results</b></p> <p>With RNfuzzyApp, we provide a user-friendly, web-based R-shiny app for differential expression analysis, as well as time-series analysis of RNA-seq data. RNfuzzyApp offers several methods for normalization and differential expression analysis of RNA-seq data, providing easy-to-use toolboxes, interactive plots and downloadable results. For time-series analysis, RNfuzzyApp presents the first web-based, automated pipeline for soft clustering with the Mfuzz R package, including methods to aid in cluster number selection, Mfuzz loop computations, cluster overlap analysis, as well as cluster enrichments.</p> <p><b>Conclusion</b></p> <p>RNfuzzyApp is an intuitive, easy to use and interactive R shiny app for RNA-seq differential expression and time-series analysis, offering a rich selection of interactive plots, providing a quick overview of raw data and generating rapid analysis results. Furthermore, its orthology assignment, enrichment analysis, as well as ID conversion functions are accessible to non-model organisms.</p>
Extended data tables to Haering and Habermann, F1000Res, RNfuzzyApp: an R shiny RNA-seq data analysis app for visualisation, differential expression analysis, time-series clustering and enrichment analysis
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GNOSIS: an R Shiny app supporting cancer genomics survival analysis with cBioPortal
<p>GNOSIS Instructional videos.</p>
Figure 8b from: Briz-Redón Á (2019) SpNetPrep: An R package using Shiny to facilitate spatial statistics on road networks. Research Ideas and Outcomes 5: e33521. https://doi.org/10.3897/rio.5.e33521
Figure 8b "Point Pattern Edition" features. - Information that is displayed (marks of the point pattern, if available, as defined by the user) when an event is clicked
Figure 5a from: Briz-Redón Á (2019) SpNetPrep: An R package using Shiny to facilitate spatial statistics on road networks. Research Ideas and Outcomes 5: e33521. https://doi.org/10.3897/rio.5.e33521
Figure 5a Example of use of the SimplifyLinearNetwork function. - A road network introduced as input in which there is an excess of road segments and vertex
Figure 1 from: Briz-Redón Á (2019) SpNetPrep: An R package using Shiny to facilitate spatial statistics on road networks. Research Ideas and Outcomes 5: e33521. https://doi.org/10.3897/rio.5.e33521
Figure 1 Workflow that describes all the steps that could be carried out in order to perform a spatial analysis on a point pattern that lies on a linear network. Some of these steps which lead to the final statistical analysis may be skipped but, at least, all of them should be considered. The blocks pointing the steps of the process include some of the R packages that would allow to successfully achieve each of them.
Figure 3b from: Briz-Redón Á (2019) SpNetPrep: An R package using Shiny to facilitate spatial statistics on road networks. Research Ideas and Outcomes 5: e33521. https://doi.org/10.3897/rio.5.e33521
Figure 3b "Network Edition" example of use (I). - Network resulting from clicking on "Rebuild linear network" in the situation of a
Figure 2a from: Briz-Redón Á (2019) SpNetPrep: An R package using Shiny to facilitate spatial statistics on road networks. Research Ideas and Outcomes 5: e33521. https://doi.org/10.3897/rio.5.e33521
Figure 2a "Network Edition" features. - Overview of the "Network Edition" section of the SpNetPrep application
Figure 6b from: Briz-Redón Á (2019) SpNetPrep: An R package using Shiny to facilitate spatial statistics on road networks. Research Ideas and Outcomes 5: e33521. https://doi.org/10.3897/rio.5.e33521
Figure 6b "Network Direction" features. - Manual addition of traffic flow to the network by using the options "Add flow" and "Add long flow"
Figure 3a from: Briz-Redón Á (2019) SpNetPrep: An R package using Shiny to facilitate spatial statistics on road networks. Research Ideas and Outcomes 5: e33521. https://doi.org/10.3897/rio.5.e33521
Figure 3a "Network Edition" example of use (I). - Use of the "Join vertex" (in green), "Remove edge" (in red) and "Add point" options (in green) in the SpNetPrep application
Figure 8a from: Briz-Redón Á (2019) SpNetPrep: An R package using Shiny to facilitate spatial statistics on road networks. Research Ideas and Outcomes 5: e33521. https://doi.org/10.3897/rio.5.e33521
Figure 8a "Point Pattern Edition" features. - An example of a point pattern that lies on a road network as it can be visualized in SpNetPrep
Figure 4b from: Briz-Redón Á (2019) SpNetPrep: An R package using Shiny to facilitate spatial statistics on road networks. Research Ideas and Outcomes 5: e33521. https://doi.org/10.3897/rio.5.e33521
Figure 4b "Network Edition" example of use (II). - Network resulting from clicking on "Rebuild linear network" in the situation of a
Figure 7 from: Briz-Redón Á (2019) SpNetPrep: An R package using Shiny to facilitate spatial statistics on road networks. Research Ideas and Outcomes 5: e33521. https://doi.org/10.3897/rio.5.e33521
Figure 7 Example of a linear road network following usual notation for the edges (\documentclass[12pt]{standalone} \usepackage{varwidth} \usepackage[utf8x]{inputenc} \usepackage[T1]{fontenc} \usepackage{lmodern} \usepackage{amsmath, amssymb, graphics, setspace} \newcommand{\mathsym}[1]{{}} \newcommand{\unicode}[1]{{}} \newcounter{mathematicapage} \begin{document} \begin{varwidth}{50in} \begin{equation*} e_{i} \end{equation*} \end{varwidth} \end{document} ) and vertex (\documentclass[12pt]{standalone} \usepackage{varwidth} \usepackage[utf8x]{inputenc} \usepackage[T1]{fontenc} \usepackage{lmodern} \usepackage{amsmath, amssymb, graphics, setspace} \newcommand{\mathsym}[1]{{}} \newcommand{\unicode}[1]{{}} \newcounter{mathematicapage} \begin{document} \begin{varwidth}{50in} \begin{equation*} v_{i} \end{equation*} \end{varwidth} \end{document} ). Arrows represent the direction of traffic flow.
Figure 6a from: Briz-Redón Á (2019) SpNetPrep: An R package using Shiny to facilitate spatial statistics on road networks. Research Ideas and Outcomes 5: e33521. https://doi.org/10.3897/rio.5.e33521
Figure 6a "Network Direction" features. - A zone of a road network introduced as an input in the "Network Direction" section of the SpNetPrep application
Figure 4a from: Briz-Redón Á (2019) SpNetPrep: An R package using Shiny to facilitate spatial statistics on road networks. Research Ideas and Outcomes 5: e33521. https://doi.org/10.3897/rio.5.e33521
Figure 4a "Network Edition" example of use (II). - Another use of the "Join vertex" (in green) option of the "Network Edition" section
Figure 5b from: Briz-Redón Á (2019) SpNetPrep: An R package using Shiny to facilitate spatial statistics on road networks. Research Ideas and Outcomes 5: e33521. https://doi.org/10.3897/rio.5.e33521
Figure 5b Example of use of the SimplifyLinearNetwork function. - Simplified version of the network in a after the application of the SimplifyLinearNetwork function with parameters Angle = 25 and Length = 65
Figure 2b from: Briz-Redón Á (2019) SpNetPrep: An R package using Shiny to facilitate spatial statistics on road networks. Research Ideas and Outcomes 5: e33521. https://doi.org/10.3897/rio.5.e33521
Figure 2b "Network Edition" features. - Example of a road network uploaded into the application
Supplementary material for the preprint "GLOSSA: a user-friendly R Shiny application for Bayesian machine learning analysis of marine species distribution"
<p>In this repository we present the code and data for the case studies in "GLOSSA: a user-friendly R Shiny application for Bayesian machine learning analysis of marine species distribution". The GLOSSA website can be accessed at https://jmestret.github.io/glossa/. Occurrence data for <em>Thunnus albacares</em> was obtained from the OBIS database (https://obis.org/taxon/127027), for <em>Caretta caretta</em> from GBIF (https://doi.org/10.15468/dl.es7562), and for <em>Siganus luridus </em>from the GreekMarineICAS geodataset (https://doi.org/10.25607/t2smha), created as part of the ALAS (Aliens in the Aegean – A Sea Under Siege) project.</p>
Data associated with "Exploring Prescribing Trends: An R Shiny App for Visualizing the Top 100 Most Commonly Prescribed Medications and Their Distribution by ATC Code"
Open the record for dataset details and reuse information.
Data associated with "RxTrends: An R Shiny Application for Visualising Open Data on Prescribed Medications in Ireland"
Open the record for dataset details and reuse information.
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.