PubMedScrapeR is a R package that will send keyword queries to PubMed, scrape all abstracts that are returned by the query, and return the most frequently occurring words associated with the keyword. Results are purely comprised of words associated with the keyword from published abstracts on PubMed.
Use devtools to install PubMedScrapeR directly from GitHub.
# if(!require(devtools)) {install.packages(devtools)}
devtools::install_github("ShanSabri/PubMedScrapeR")
> library(PubMedScrapeR)
> results <- PubMedScrapeR::PubMedScrapeR(keyword = c("Shan Sabri", "asdfjkj;", "Nanog"),
top_n = 2000,
verbose = FALSE)
2019-08-09 15:47:59 - Shan Sabri
2019-08-09 15:48:01 - asdfjkj;
2019-08-09 15:48:02 - asdfjkj; - No abstracts found!
2019-08-09 15:48:02 - Nanog
> lapply(results, head, n = 20)
[[1]]
Shan Sabri_6
cell 20
cells 12
somatic 8
expression 7
pluripotency 7
stem 7
gata6 6
hescs 6
naive 6
osk 6
cardiac 5
development 5
enhancer 5
reprogramming 5
tfs 5
cardiomyocytes 4
embryonic 4
cellular 3
cycle 3
discrete 3
[[2]]
[1] NA
[[3]]
Nanog_5200
cells 21642
cell 12799
stem 10404
expression 9886
cancer 4558
differentiation 4459
oct4 4336
pluripotency 3902
genes 3776
embryonic 3665
markers 3573
sox2 3396
gene 2962
pluripotent 2740
factors 2573
transcription 2503
tumor 2201
induced 2160
protein 2095
mouse 2020Pull requests are welcome. For major changes, please open an issue first to discuss what you would like to change.
Please make sure to update tests as appropriate.