A python package using rpy2 to port DESeq2 into python.
Dependencies are pandas (python), rpy2 (python), and DESeq2 (R)
Best way to build dependencies should be via conda.
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
conda create -q -n diffexpr python=3.6 \
pandas tzlocal rpy2 biopython ReportLab pytest-cov \
bioconductor-deseq2 codecov
conda activate diffexpr # activate diffexpr environment
Rscript setup.R #to install DESeq2 correctly
python setup.py install
An example of running DESeq2 in python using diffexp package is provided here.