GENOVA 
Explore the Hi-Cs!
The increase in interest for Hi-C methods in the chromatin community has led to a need for more user-friendly and powerful analysis methods. The few currently available software packages for Hi-C do not allow a researcher to quickly summarize and visualize their data. An easy to use software package, which can generate a comprehensive set of publication-quality plots, would allow researchers to swiftly go from raw Hi-C data to interpretable results.
Here, we present GENome Organisation Visual Analytics (GENOVA): a software suite to perform in-depth analyses on various levels of genome organisation, using Hi-C data. GENOVA facilitates the comparison between multiple datasets and supports the majority of mapping-pipelines.
GENOVA directly reads data from:
- HiC-pro
- cooler
- juicer
Installation
You can install GENOVA from GitHub with:
# install.packages("remotes")
remotes::install_github("robinweide/GENOVA")Note to long-time users
Version 1.0 will contain a massive overhaul, which will result in
breaking nearly every analysis. To provide legacy support, we made the
ye olde
lighthouse
release. This can be installed with
devtools::install_github("robinweide/GENOVA@v0.95"). Furthermore, if
you have custom scripts based on the output of construct.experiment(),
you can use v1 and set legacy=TRUE in loadContacts() to get a
similar output. This, of course, also allows you to load .cooler and
.hic files in pre-v1 versions 👍.
Support
We have provided a quite lengthy vignette, so please read that first. If there are still unanswered questions, please use the issue-tracker.
Publication
Please see our preprint on bioRxiv: Hi-C Analysis with GENOVA: a case study with cohesin variants.
Code of conduct
Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.