Authors: Francis Bourassa (@francis-B)
Email: [email protected]
This repository contains the scripts used to produce heatmaps and wordclouds of ARTICLENAME.
The PubMed Corpus files were converted to tsv files using a modified version of the medline-pubmed-extractor tool developped by Sahan Serasinghe (@sahansera) and the keywords were searched in these tsv with a modified version of the pubmed_trend_analysis tool developped by lab42OPEN. Both modified versions can be found in tool/.
To reproduce the analysis, one can use the analyse_pubmed.sh which download the Pubmed Corpus files and call the tools mentionned above. Finally, the output of pubmed_trend_analysis, which can be found in results/, can be analysed with the create_heatmaps.R and create_wordclouds.py scripts to reproduce the figures.
To ease the last step, the conda environnements used to run the R and python scripts can be found in conda/.