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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:

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.

ljc
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    why the downvotes? If you've got a better solution, by all means please post them, but subprocessing out doesn't seem very Pythonic to me. – ljc Mar 30 '16 at 10:40
  • Subprocessing is totally Pythonic imho, because Python is a great language for scripting and pipelining. You are trying to make your life harder. Why the downvotes, though. – JulienD Mar 30 '16 at 11:24
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    possible reason for downvote: `Questions asking us to recommend or find a book, tool, software library, tutorial or other off-site resource are off-topic for Stack Overflow as they tend to attract opinionated answers and spam. ` – rawr Mar 30 '16 at 11:38
  • I took this question over to Biostars, if anyone has the need to further discuss this topic. https://www.biostars.org/p/9495368/ – ljc Oct 28 '21 at 06:42

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