This repository contains helper functions and Rmarkdown files for the analysis is i/eCLIP dataset using data post-processing package htseq-clip and statistical analysis package DEWSeq.

This repository is organized as follows:

• htseq-clip_snakemake contains snakemake pipleline for post-processing eCLIP datasets using htseq-clip.
• Parametrized_Rmd contains an Rmd file called analyseStudy.Rmd which can be used to analyze eCLIP datasets. Further details are available in the README file in the folder.
• SLBP_analysis contains Rmarkdwon file, and knitted html and pdf outputs for the analysis of ENCODE SLBP eCLIP data using DEWSeq.
• Volcano_plot contains an Rscript called volcanoplot.R, which can be used to create volcano plots of significant windows. For further details, please read the README file in the folder.