3
$\begingroup$

The R package limma is ideal to perform differential expression analysis. Is there any limma alternative in Python?

I'm trying to use statsmodels and scikitlearn in conjunction with some other cool tools (such as pycombat) to get limma-like workflows. However, I'm missing many capabilities from the limma toolbox.

Improve this question
$\endgroup$
3
  • 1
    $\begingroup$ Is there a possibility for you to call R from Python? If so you can try Rpy2 (pypi.org/project/rpy2) $\endgroup$
    – plat
    Aug 11, 2021 at 6:24
  • 1
    $\begingroup$ That's true. You can always wrap Python around R. For example, if working with limma, you can use Python to prepare the pieces that limma needs to create an Expression Set object with the ExpressionSet() function (expression, phenotype and feature data). However you will be always forced to write the limma workflow using R syntax. In any case I will give it a try! Many Thanks! $\endgroup$
    – Gian Arauz
    Aug 11, 2021 at 8:44
  • 1
    $\begingroup$ I am working on EXACTLY this thing. My methylize python package supports some of these functions, but I found this while looking for packages that might give me idea about what features people want. $\endgroup$
    – Marc Maxmeister
    Feb 18, 2022 at 17:27

1 Answer 1

Reset to default
2
$\begingroup$

August 2021

To date, it seems that the response to this question is "No". However, there is a GitHub repository called edgePy, aiming to "become an implementation of edgeR for differential expression analysis in the Python language" (edgeR is somewhat similar to limma).

PS: Many thanks to @ATpoint90 (the Twitter "hive mind" summoner) and @sridnona6 (edgePy developer).

Improve this answer
$\endgroup$

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service and acknowledge that you have read and understand our privacy policy and code of conduct.

Not the answer you're looking for? Browse other questions tagged or ask your own question.