This package provides functions for analyzing genomic regions:
There are functions doing:
- Basic statistics of regions such as proportion in genome or numbers of regions in each sample
- General region finder which looks for genomic regions with certain features
- Annotation to gene model / genomic features
- Correlation / enrichment to genomic features
- Subgroup specific regions
- Hilbert curve visualization, support multiple layers
- Heatmap with alignment to certain genomic feature, such as methylation around CpG island.
GREAT (Genomic Regions Enrichment of Annotations Tool, http://great.stanford.edu) is a popular web-based tool to associate biological functions to genomic regions. The **rGREAT** package makes GREAT anlaysis automatic by first constructing a HTTP POST request according to user's input and retrieving results from GREAT web server afterwards.
Trellis graph is a type of graph which splices data by variables and visualize subset of data in each category parallel. The advantage of Trellis graph is that it can easily reveal multiple variable relationship behind the data. Here, **gtrellis** provides a flexible way to arrange genomic categories and support adding self-defined graphics on the plot.
This R package implements circular visualization in R. Due to the natural born feature of R to draw statistical graphics, this package can provide a more general and flexible way to visualize huge information in a circular style.
Zuguang Gu, Lei Gu, Roland Eils, Matthias Schlesner, and Benedikt Brors. circlize implements and enhances circular visualization in R. Bioinformatics (2014) 30 (19): 2811-2812, 2014 doi:10.1093/bioinformatics/btu393