CoNekT Grasses derives from CoNekT (Co-expression Network Toolkit), described in Proost et al. 2018 (https://doi.org/10.1093/nar/gky336), an interactive and open-source web server dedicated to grasses expression data analysis.
- The Basics
- Expression profiles, heatmaps and specificity
- Gene Families and Phylogenetic trees
- Comparing specificity
- Coexpression Networks and Clusters
CoNekT Grasses currently requires Python 3.8. To install Python 3.8 execute the following codes:
sudo add-apt-repository ppa:deadsnakes/ppa
sudo apt-get update
sudo apt-get install python3.8Dependencies are usually installed using apt and pip:
sudo apt install python3.8-venv python3.8-dev
python3.8 -m ensurepip --default-pip
python3.8 -m pip install --upgrade pip setuptools wheel
pip3 install virtualenvTo set up the environment from the root directory of the repository, run:
virtualenv --python=python3.8 CoNekT
source CoNekT/bin/activate
sudo apt-get install python3.8-dev libmysqlclient-dev apache2 apache2-dev libapache2-mod-wsgi-py3
cd ../
pip3 install -r requirements.txtNext steps:
Documentation can be generated using Sphinx.
To generate the documentation, run:
cd CoNekT/docs/
sphinx-build -b html source/ build/Note that we changed the default Sphinx builder to use the Markdown parser. This is done by adding the following line to conf.py file in the CoNekT/docs folder:
extensions = ["myst_parser"]
- Dr. Renato Augusto Correa dos Santos
- Prof. Dr. Diego M. Riaño-Pachón (group leader)
- Felipe Vaz Peres
- Jorge Muñoz
- David Texeira Ferraz
- Bianca Santos Pastos
- Arthur Shuzo Owtake Cardoso