any recommended tools for batch effect and normalization not written in R?

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7.1 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?

R RNA-Seq combat python batch-effect • 3.4k views

ADD COMMENT • link updated 8 hours ago by Ram 43k • written 7.1 years ago by dyollluap ▴ 310

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Why the aversion to R, if I may ask...

ADD REPLY • link 7.1 years ago by Benn 8.3k

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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.

ADD REPLY • link 7.1 years ago by dyollluap ▴ 310

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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.

ADD REPLY • link 7.1 years ago by andrew.j.skelton73 6.5k

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

ADD REPLY • link 7.1 years ago by O.rka ▴ 710

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