This is the Knowledge Engine for Genomics (KnowEnG), an NIH BD2K Center of Excellence, Pipelines Notebooks.
There are two jupyter notebooks that one can choose from:
Notebook | Pipeline | Parameters |
---|---|---|
Signature_Analysis_Pipeline_notebook | Signature_Analysis_Pipeline | Signature Analysis parameter files |
Kaplan_Meier | Independent notebook | notebook settings |
pip3 install pyyaml
pip3 install xmlrunner
pip3 install knpackage
pip3 install scipy==0.18.0
pip3 install numpy==1.11.1
pip3 install pandas==0.18.1
pip3 install matplotlib==1.4.2
pip3 install scikit-learn==0.17.1
apt-get install -y python3-pip
apt-get install -y libfreetype6-dev libxft-dev
apt-get install -y libblas-dev liblapack-dev libatlas-base-dev gfortran
2. Install jupyter notebook. ( http://jupyter.readthedocs.io/en/latest/install.html )
pip3 install --upgrade pip
pip3 install jupyter
git clone https://github.com/dlanier/notebooks_KnowEnG.git
git clone https://github.com/KnowEnG/Signature_Analysis_Pipeline.git
cd (clones location)/Signature_Analysis_Pipeline/test
make env_setup
cd ../../notebooks_KnowEnG/test/
make env_setup
cd run_dir
jupyter notebook