search

CredibilityLab / groundhog

Reproducible R Scripts Via Date Controlled Installing & Loading of CRAN & Git Packages
https://groundhogr.com/
GNU General Public License v3.0
78 stars 4 forks source link

Bioconductor support #76

Closed jasonbosch closed 2 years ago

jasonbosch commented 2 years ago

This looks like an interesting (and important) package but, currently, it will only go part-way to solving reproducible code in biological scripts. Many R scripts by biologists will use packages from Bioconductor (https://bioconductor.org/). I'm not sure whether the authors include biologists or not but I saw no mention of Bioconductor in either the Data Colada posts or the Groundhog website. Are there plans to include support for Bioconductor packages in the future?

urisohn commented 2 years ago

Yes, that's the next major change planned. Hopefully this summer

jasonbosch commented 2 years ago

That sounds great! I will definitely need to try it out then. It will also save me needing to specify package versions in my methods section (which few authors seem to do).

AlexPars commented 1 year ago

Is there an update regarding groundhog package's capability to incorporate R packages from BioConductor? I did not find any mention of it in latest version of groundhog package, and I am not sure if I have missed something

On a side note, groundhog is a very useful package, especially with the demise of checkpoint and MRAN

urisohn commented 1 year ago

i was planning to do that this april/may, but with MRAN disappearing it lost priority. Next time i return to working on groundhog i plan on doing it, perhaps around October of this year, but no promises. If someone wants to collaborate and chip in with coding that would be welcomed too

Lukas-1 commented 1 year ago

It would be amazing to have groundhog for Bioconductor. There are just so many advantages over renv.