The package intePareto will be updated and maintained here not on CRAN anymore.
intePareto is designed to prioritize genes with consistent changes in RNA-Seq and ChIP-Seq data of different histone modifications betweeen different conditions using Pareto optimization.
The intePareto workflow starts with RNA-Seq and ChIP-Seq data for two different cell types or conditions. The ChIP-Seq data will in general comprise information on several histone modifications with activating or repressing function. The end product of intePareto is a list of genes prioritized according to congruence of changes of gene expression and histone modifications.
The detailed example of using intePareto is shown in this case study example.