shinyPubMed allows users to search and visualize PubMed articles based on specific search terms and a date range. It displays article details, a line chart of publications per year, and a word cloud generated from the abstracts.
This Shiny app is designed to provide an interactive interface for searching and analyzing PubMed articles. Users can enter specific search terms and select a date range to retrieve relevant articles. The app presents this data in a tabular format, along with visualizations like a yearly publication trend line chart and a word cloud representing the most frequent terms in the abstracts. This tool is particularly useful for researchers and academics in the field of biomedical sciences.
To run this Shiny application, you will need R v4.3.2 installed on your system with the following R packages: shiny, rentrez, dplyr, DT, XML, ggplot2, and wordcloud2. You can install these packages using the R command install.packages("package_name").
install.packages(c("shiny", "rentrez", "tidyverse", "DT", "XML", "wordcloud"))- Launch the App: Run the Shiny app script in RStudio or in an R environment.
- Enter Search Terms: Input your desired search terms in the provided field, separated by commas.
- Set Date Range: Choose the start and end years for your article search.
- Search and Visualize: Click the 'Search' button to fetch the articles. The results will be displayed in a data table, and the visualizations will be available under the 'Visualization' tab.
- Download Data: You can download the fetched data as a CSV file using the 'Download Data' button.
To run the app from GitHub, use the below code:
# Load the shiny package
if (!requireNamespace("shiny", quietly = TRUE)) {
install.packages("shiny")
}
library(shiny)
# Run the app from a GitHub repository
runGitHub("shinyPubMed", "sdhutchins")