Improved analysis of (e)CLIP data with RCRUNCH yields a compendium of RNA-binding protein binding sites and motifs

This repo contains materials associated with the publication "Improved analysis of (e)CLIP data with RCRUNCH yields a compendium of RNA-binding protein binding sites and motifs". v1.0.0 of RCRUNCH was used and the scripts associated with all of the analyses are included in respective folders along with config files.The main folders are:

genomewise_posteriors: genome-wide predictions of binding sites for RBPs used in benchmarking, done with the MotEvo.

tool.rcrunch_rbp_subset: RCRUNCH runs for the subset of ENCODE samples corresponding to the RBPs that were used compare the performance of computational analysis methods. The RBPs are: PUM2, RBFOX1, PTBP1 and HNRNPC.

RCRUNCH_benchmark: predicted peaks for the datasets mentioned above, generated by tools other than RCRUNCH. The same input files (result of preprocessing) as in rcrunch_rbp_subset were used, except for CLIPper, for which the ENCODE-reported peaks were used

rcrunch_encode: RCRUNCH peak predictions for all eCLIP samples available in ENCODE.