mworkman13/HiCAGE: Hi-C Annotation and Graphics Ensemble

This package takes chromsome conformation capture data as input and annotates each genomic region with segmentation data from StateHub (http://statehub.org/statehub/), for example. This data can then be annotated with the nearest gene and using RNA-seq data, expression values can be linked to each gene. Moreover, these data can be combined into a circle plot with heatmaps showing average score of chromsome conformation capture interaction between segmentation marks as well as average FPKM values for genes in each type of interaction.

install.packages("remotes")
remotes::install_github("mworkman13/HiCAGE")