tpall / entrezquery

Query entrez databases using R, returns document summaries as data frame. Wrapper function around esearch and esummary etools.

Get document summaries for your entrez query

Run entrez database query. Wrapper around entrez esearch and esummary tools. Returns document summaries for query Ids in a data frame.

devtools::install_github("tpall/entrezquery")
library(entrezquery)

## Search GEO database
q <- "expression profiling by high throughput sequencing[DataSet Type]"
geo <- entrez_docsums(q, db = 'gds', retmax = 10)
geo

## Search Pubmed
q <- "science[journal] AND breast cancer AND 2016[pdat]"
pm <- entrez_docsums(query = q, db = "pubmed", retmax = 10)
pm