Extract data from a PDF file with Tabula
Kirkham et al. 2006 is a prospective 2-year study of 60 patients with rheumatoid arthritis (RA). It shows that “synovial membrane cytokine mRNA expression is predictive of joint damage progression in RA”. The PDF includes a few tables with data on cytokine measurements and correlations with joint damage. Here, we’ll use Tabula to extract data from tables in the PDF file. Then we’ll make figures with R.
Get human transcription factor target genes
I made a data package with human transcription factor target genes for use in R. It is a collection of data from three sources: TRED, ITFP, and ENCODE. I use them to test if the targets of a transcription factor are differentially expressed in my data. Also, I can test if a set of transcription factor target genes is enriched for some gene set of interest.