https://github.com/sdhutchins/shinypubmed
shinyPubMed allows users to search and visualize PubMed article abstracts based on specific search terms and a date range.
https://github.com/sdhutchins/shinypubmed
pubmed rshiny shiny-apps
Last synced: about 2 months ago
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shinyPubMed allows users to search and visualize PubMed article abstracts based on specific search terms and a date range.
- Host: GitHub
- URL: https://github.com/sdhutchins/shinypubmed
- Owner: sdhutchins
- License: mit
- Created: 2023-12-17T18:48:29.000Z (almost 2 years ago)
- Default Branch: main
- Last Pushed: 2024-08-28T23:44:42.000Z (about 1 year ago)
- Last Synced: 2025-04-07T21:18:11.642Z (7 months ago)
- Topics: pubmed, rshiny, shiny-apps
- Language: R
- Homepage: https://connect.posit.cloud/sdhutchins/content/01919b57-c478-321e-5b24-60591296013d
- Size: 78.1 KB
- Stars: 1
- Watchers: 2
- Forks: 0
- Open Issues: 5
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# shinyPubMed
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.
## Table of Contents
- [App Background](#app-background)
- [Install & Setup](#install-setup)
- [Usage](#usage)
- [Authors](#authors)
- [License](#license)
## App Background
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.
## Install & Setup
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")`.
```r
install.packages(c("shiny", "rentrez", "tidyverse", "DT", "XML", "wordcloud"))
```
## Usage
1. **Launch the App**: Run the Shiny app script in RStudio or in an R environment.
2. **Enter Search Terms**: Input your desired search terms in the provided field, separated by commas.
3. **Set Date Range**: Choose the start and end years for your article search.
4. **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.
5. **Download Data**: You can download the fetched data as a CSV file using the 'Download Data' button.
### Run App from GitHub
To run the app from GitHub, use the below code:
```r
# Load the shiny package
if (!requireNamespace("shiny", quietly = TRUE)) {
install.packages("shiny")
}
library(shiny)
# Run the app from a GitHub repository
runGitHub("shinyPubMed", "sdhutchins")
```
## Authors
* [Shaurita D. Hutchins](mailto:shaurita.d.hutchins@gmail.com)
## License
[MIT License](LICENSE)