[Bioc-devel] Integrating python into an R package

Vincent Carey @tvjc @end|ng |rom ch@nn|ng@h@rv@rd@edu
Tue Feb 18 17:08:33 CET 2020

I would advise that you do not reimplement working methods but interface to
them.  Bioconductor's BiocSklearn package
exposes aspects of scikit and you could have a look at that for one
approach.  The basilisk package <https://github.com/LTLA/basilisk> in
development is
a more systematic way of governing interoperability with python and should
also be examined.

On Tue, Feb 18, 2020 at 10:53 AM Zhang, David <david.zhang.12 using ucl.ac.uk>

> Dear all,
> I’m a bioinformatics PhD student at UCL who’s recently been trying to
> develop an R package that has some python dependencies. Specifically, areas
> of my current pipeline are written in python for speed and any ML has been
> implemented through sklearn. I was wondering what you would advise as the
> best practice of integrating python code into Bioconductor/R p
> packages? E.g. R to python interfaces (such as reticulate) or advising
> package users to call python scripts independently or re-writing python
> code in R?
> Any advice would be much appreciated.
> Many thanks in advance,
> David
> _______________________________________________
> Bioc-devel using r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

The information in this e-mail is intended only for the ...{{dropped:18}}

More information about the Bioc-devel mailing list