NOTE: we have discontinued gpseqc in favor of the faster R script GPSeq-RadiCal.

gpseqc

A Python3 package that provides tools to estimate the 3D spatial nuclear centrality of genomic regions and compare different centrality rankings.

• Read the (public) documentation for more details.
• Read the (private) documentation for more details.
  Once the repo goes public, private docs will be merged with public ones.

Installation

To install, run the following:

git clone http://github.com/ggirelli/gpseqc
cd gpseqc
sudo -H pip3 install .

To test your installation, run: pytest-3 --pyargs gpseqc.

To uninstall run the following from within the repository folder:

sudo -H pip3 uninstall gpseqc

To update, first uninstall, and then run the following from within the repository folder.

git pull
sudo -H pip3 install .

Additional dependencies

Most of the required dependencies are automatically install by pip3. Still, some require some manual steps. Specifically, gpseqc requires the following packages:

• tkinter

That on Ubuntu can be easily installed with:

sudo apt install python3-tk

Usage

Estimate centrality

The gpseqc_estimate script allows to estimate regional nuclear centrality based on a multi-condition GPSeq experiment. Run gpseqc_estimate -h for more details.

Compare centrality ranks

The gpseqc_compare script allows to compare different regional centrality ranks. Run gpseqc_compare -h for more details.

Contributing

We welcome any contributions to GPSeqC. Please, refer to the contribution guidelines if this is your first time contributing! Also, check out our code of conduct.

License

MIT License
Copyright (c) 2017-18 Gabriele Girelli