lux563624348 / diffexpr

Porting DESeq2 and DEXSeq into python via rpy2

diffexpr

A python package using rpy2 to port DESeq2 into python.

INSTALL

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

Example

An example of running DESeq2 in python using diffexp package is provided here.