any recommended tools for batch effect and normalization not written in R?
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4.6 years ago
dyollluap ▴ 310

Are there any existing tools for RNA-seq batch effect normalization that don't require transformation into an R data structure?

I have found a python wrapper for R combat, though I'd like to move away from the R dependency and preferably utilize python libraries. Does anyone have a tool/script for this already?

RNA-Seq batch effect combat python R • 2.6k views
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Why the aversion to R, if I may ask...

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it's not an aversion to R, I appreciate the value of R based methods and any/all open source bioinformatic resources. In this case I'm looking for an alternative option that could be tied in with other existing frameworks that are already heavily invested in python methods.

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I'm not aware of a python implementation limma, or ComBat for that matter, so it seems RPy2 would be your friend in this case.

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Did you find anything? Also, what is the model matrix in https://github.com/brentp/combat.py?

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