PRECISE_figures

Jupyter notebooks and code to reproduce figures.

TO DO before launching the notebooks

• Install all the dependencies sh setup.sh

• Install GSEA package (Java implementation) [Subramanian et al 2005] available at the following address:

http://software.broadinstitute.org/gsea/msigdb/download_file.jsp?filePath=/resources/software/gsea-3.0.jar

This has to be put in the root folder.

• Clone ComBat version using Brent Pedersen implementation donwloadable as this location:

git clone https://github.com/brentp/combat.py

mv combat.py combat

• Install statannot using Marc Weber implementation:

conda activate precise_figures

pip install git+https://github.com/webermarcolivier/statannot

conda deactivate