GENOVA(2)

🍴Fork Note

This repository is a fork of the original GENOVA work. All credit for the idea and original content of the application goes to the original authors, please direct all questions concerning the package to them.
The portions of code that were added are noted below in the 'Changes' section, and are also clearly marked in the source.

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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 (enhanced normalization options)
• juicer

Changes

In this fork, the loadCooler function in loading_cooler.R has a new parameter, weight, which is the string name of the normalization column within your .cool file.
A call to loadCooler would look like:

loadCooler("/path/to/file.cool",
            balancing = TRUE,
            scale_bp = NULL,
            scale_cis = FALSE,
            resolution = 5000,
            weight = "VC_SQRT")

• ✅ Added support for custom normalization schemes in loadCooler()
• 🔁 Refactored balance_cooler() to handle missing weights gracefully

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.

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