This is a R package for automatical data annotation with terms in a dictionary. The main function is 'CountTermsInStudies'. It takes 'searchingData' to search from as either data frame/matrix or a link to the data in 'tsv','csv' or 'txt' formate. It also takes another parameter 'dictionary', which could be any dictionary with one name column and one search term (regular expression accepted) column. Please refer to manual for specific header names.

install.packages("devtools")
devtools::install_github("shihikoo/AutoAnnotation")

Code calls 'pdftotext' to convert pdf to text.

One may download the Xpdf command line tools at https://www.xpdfreader.com/download.html And add the software path to parameter 'conversionSoftware'.

The package is at alpha testing stage.