Differential gene expression analysis in Python

Question

[Leendert]

It seems that most differential gene expression packages for RNA-Seq are written in R.

Examples include:

• edgeR
• limma
• DESeq

Are any similar (and easy to use) packages available for Python, or have any of the R packages been ported?

The best I could find was:

• https://bcbio.wordpress.com/2009/09/13/differential-expression-analysis-with-bioconductor-and-python/
• http://dept.stat.lsa.umich.edu/~kshedden/Python-Workshop/gene_expression_comparison.html

But I really don't want to use rpy2 (_1st link_). The second link is probably where I would start, but I first wanted to make sure I'm not reinventing the wheel.

SIDE NOTE:

This question was asked on Stackoverflow (https://stackoverflow.com/questions/36305682/differential-gene-expression-analysis-in-python), but closed because your not allowed to ask for suggestions on tools (please explain all the upvotes then), but in any case, I thought I'd bring it over to this forum for suggestions.

[Antonio R. Franco]

The only comment I would like to express is that you should take into account that the mentioned tools working under R are very well known, have been used in a miriad of experiments, have their sources publicly available so they have been analyzed by many potential users, and because of that, they are the recommended for most of the cases.

[fracarb8]

scanpy uses diffxpy to run DE analysis, BUT, keep in mind that scanpy is for single-cell RNA-Seq, not bulk.