NOTE: we have discontinued gpseqc
in favor of the faster R script GPSeq-RadiCal.
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:
tkinter
That on Ubuntu can be easily installed with:
sudo apt install python3-tk
The gpseqc_estimate
script allows to estimate regional nuclear centrality based on a multi-condition GPSeq experiment. Run gpseqc_estimate -h
for more details.
The gpseqc_compare
script allows to compare different regional centrality ranks. Run gpseqc_compare -h
for more details.
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.
MIT License
Copyright (c) 2017-18 Gabriele Girelli