<p><strong>August 2021</strong></p>
<p>To date, it seems that the response to this question is <strong>&quot;No&quot;</strong>. However, there is a GitHub repository called <a href="https://github.com/r-bioinformatics/edgePy" rel="nofollow noreferrer"><code>edgePy</code></a>, aiming to <em>&quot;become an implementation of <a href="https://bioconductor.org/packages/release/bioc/html/edgeR.html" rel="nofollow noreferrer"><code>edgeR</code></a> for differential expression analysis in the Python language&quot;</em> (<code>edgeR</code> is somewhat similar to <code>limma</code>).</p>
<p>PS: Many thanks to @ATpoint90 (the Twitter <a href="https://twitter.com/ATpoint90/status/1423669033702940678" rel="nofollow noreferrer">&quot;hive mind&quot; summoner</a>) and @sridnona6 (<code>edgePy</code> developer).</p>

CC BY-SA 4.0
2021-08-07T18:08:00.623Z
2021-08-11T01:37:57.120Z
2021-08-11T01:37:57.120Z
Gian Arauz
<p>The R package <a href="https://bioconductor.org/packages/release/bioc/html/limma.html" rel="nofollow noreferrer"><code>limma</code></a> is ideal to perform differential expression analysis. Is there any <code>limma</code> alternative in Python?</p>
<p>I'm trying to use <a href="https://www.statsmodels.org/stable/index.html" rel="nofollow noreferrer"><code>statsmodels</code></a> and <a href="https://scikit-learn.org/stable/" rel="nofollow noreferrer"><code>scikitlearn</code></a> in conjunction with some other cool tools (such as <a href="https://github.com/epigenelabs/pyComBat" rel="nofollow noreferrer"><code>pycombat</code></a>) to get <code>limma</code>-like workflows. However, I'm missing many capabilities from the <code>limma</code> toolbox.</p>

CC BY-SA 4.0
2021-08-11T06:24:36.823Z
Is there a possibility for you to call R from Python? If so you can try Rpy2 (https://pypi.org/project/rpy2/)
jxx_fa
CC BY-SA 4.0
2021-08-11T08:44:47.447Z
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!
Gian Arauz
CC BY-SA 4.0
2022-02-18T17:27:03.243Z
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.
Marc Maxmeister
<r><python><differential-expression><limma>
R limma alternatives in Python
# R limma alternatives in Python

(Asked by: username_0 on 2021-08-06)

The R package [`limma`](https://bioconductor.org/packages/release/bioc/html/limma.html) is ideal to perform differential expression analysis. Is there any `limma` alternative in Python?

I'm trying to use [`statsmodels`](https://www.statsmodels.org/stable/index.html) and [`scikitlearn`](https://scikit-learn.org/stable/) in conjunction with some other cool tools (such as [`pycombat`](https://github.com/epigenelabs/pyComBat)) to get `limma`-like workflows. However, I'm missing many capabilities from the `limma` toolbox.

**Tags:** r, python, differential-expression, limma
> **Comments:**
> **username_1**: Is there a possibility for you to call R from Python? If so you can try Rpy2 (https://pypi.org/project/rpy2/)  
> **username_0**: 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!  
> **username_2**: 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.  

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## 1 answers

### Answer by username_0 on 2021-08-07. Score: 2 | Accepted answer

**August 2021**

To date, it seems that the response to this question is **"No"**. However, there is a GitHub repository called [`edgePy`](https://github.com/r-bioinformatics/edgePy), aiming to *"become an implementation of [`edgeR`](https://bioconductor.org/packages/release/bioc/html/edgeR.html) for differential expression analysis in the Python language"* (`edgeR` is somewhat similar to `limma`).

PS: Many thanks to @ATpoint90 (the Twitter ["hive mind" summoner](https://twitter.com/ATpoint90/status/1423669033702940678)) and @sridnona6 (`edgePy` developer).


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