Bioconductor packages This respository contains R code and Bioconductor packages used for differentially methylated regions (DMR) and gene set enrichment analysis for putative promoters in the African cheetah. The DMR core analysis was customized based on https://github.com/skinnerlab/MeDIP-seq. The functional and regional annotation as well as the enrichment analysis were put together based on pre-existing Bioconductor packages.
This code allows to analyze data from any non-model mammalian system with a reference genome even if it is only on scaffold level assembly.
COMMING SOON: AN UPDATED VERSION WHICH INCLUDES MODEL FITTING, ENRICHMENT ANALYSIS BASED ON SEQUENCE ALIGNMENT AND EPIGENOME-WIDE ASSOCIATION STUDIES