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.

Getting started

Package details

Bioconductor views ChIPSeq DNA3DStructure FunctionalPrediction GUI GeneExpression GenomeAnnotation HiC Visualization
MaintainerMichael Workman <[email protected]>
LicenseGPL (>= 3)
Version1.0.0
Package repositoryView on GitHub
Installation Install the latest version of this package by entering the following in R:
install.packages("devtools")
library(devtools)
install_github("mworkman13/HiCAGE")
mworkman13/HiCAGE documentation built on Sept. 24, 2018, 10:12 p.m.