[Bioc-devel] Bioconductor guidelines for R and Julia integration

[Jennifer Wokaty]

Hi Fabricio,

We don't currently have any guidelines for working with Julia, so working with JuliaCall seems fine. We can install Julia on the builders when you submit your package. Thanks for your question.

Jennifer Wokaty
they/them
Bioconductor Core Team
CUNY SPH

________________________________________
From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Fabricio de Almeida <fabricio_almeidasilva using hotmail.com>
Sent: Thursday, March 31, 2022 12:55 PM
To: Bioc-devel using r-project.org
Subject: [Bioc-devel] Bioconductor guidelines for R and Julia integration

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Dear Bioc developers,

I am currently working on a package for network analysis, and one of the main functions takes a long time to run in real data sets. Rewriting it in Julia leads to a dramatic reduction in runtime, so I think it could be a feasible solution.

I know there are some guidelines for handling C and Fortran code in Bioc packages (https://urldefense.proofpoint.com/v2/url?u=https-3A__bioconductor.org_developers_package-2Dguidelines_&d=DwIFAw&c=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY&r=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA&m=kabUjXz3P3XfU3BR7xG_twMdSacOOfyzmI-c4hZs5dI&s=juTDbpZW0NSTvIQGM8MGfRvWWptd0h8jg4mh2St1biw&e= ), as well as for Python code (using {basilisk}), but I have never seen anything similar for Julia.

I know Julia code can be integrated in R with the JuliaCall package (https://urldefense.proofpoint.com/v2/url?u=https-3A__cran.r-2Dproject.org_web_packages_JuliaCall_index.html&d=DwIFAw&c=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY&r=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA&m=kabUjXz3P3XfU3BR7xG_twMdSacOOfyzmI-c4hZs5dI&s=cu3XlKpY4hRDe2kaPEWGY6XWxVh6QebDLqg2BRE5A6M&e= ), but I don't know what is the standard practice in Bioc. Could anyone help me on that?

Kind regards,
Fabricio


=========================


Fabr�cio de Almeida Silva, MSc.

PhD student in Bioinformatics (Ghent University, Belgium)

UGent-VIB Center for Plant Systems Biology

Personal website: https://urldefense.proofpoint.com/v2/url?u=https-3A__almeidasilvaf.github.io&d=DwIFAw&c=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY&r=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA&m=kabUjXz3P3XfU3BR7xG_twMdSacOOfyzmI-c4hZs5dI&s=ThuOXlUQqrDT1NcndRUaTSxN0bmhlRWtX5vdaAsZdIE&e=


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