GPSeq-based centrality estimation.
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.
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 .
Most of the required dependencies are automatically install by
pip3. Still, some require some manual steps. Specifically,
gpseqc requires the following packages:
That on Ubuntu can be easily installed with:
sudo apt install python3-tk
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
gpseqc_compare script allows to compare different regional centrality ranks. Run
gpseqc_compare -h for more details.
MIT License Copyright (c) 2017-18 Gabriele Girelli
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