PT  - JOURNAL ARTICLE
AU  - Michael J. Workman
AU  - Tiago C. Silva
AU  - Simon G. Coetzee
AU  - Dennis J. Hazelett
TI  - <em>HiCAGE</em> : an R package for large-scale annotation and visualization of 3C-based genomic data
AID  - 10.1101/315234
DP  - 2018 Jan 01
TA  - bioRxiv
PG  - 315234
4099  - http://biorxiv.org/content/early/2018/05/05/315234.short
4100  - http://biorxiv.org/content/early/2018/05/05/315234.full
AB  - Chromatin interactions measured by the 3C-based family of next generation technologies are becoming increasingly important for measuring the physical basis for regulatory interactions between different classes of functional domains in the genome. Software is needed to streamline analyses of these data and integrate them with custom genome annotations, RNA-seq, and gene ontologies. We introduce a new R package compatible with Bioconductor—Hi-C Annotation and Graphics Ensemble (HiCAGE)—to perform these tasks with minimum effort. In addition, the package contains a shiny/R web app interface to provide ready access to its functions.Availability and Implementation The software is implemented in R and is freely available under GPLv3. HiCAGE runs in R (version 3.4) and is freely available through github (https://github.com/mworkman13/HiCAGE) or on the web (https://junkdnalab.shinyapps.io/hicage).