Using the rentrez R package to search PubMed to plot the number of papers by year (CC212)

May 12, 2022 • PD Schloss • 1 min read • •

Pat will show you how to search PubMed from R using the rentrez package to understand how the number of papers in a field has grown over time. He’ll share two ways. First, he’ll get the data directly from PubMed and import them into R. Second, he’ll automate the process using the rentrez R package, which allows you to search PubMed and any NCBI database from within R. Along the way, he’ll show how to analyze the data using R functions from dplyr and ggplot2 within RStudio.

Code

You can browse the state of the repository at the

• beginning of the episode
• end of the episode