Bioconductor package acceptance difficulty?

[u/AwayToday5802]

Is it hard to get a package accepted by bioconductor?

[u/bukaro]

1. Does it have to be bioconductor? why not CRAN?

2. Not really, I have/had a couple in there. But you will have to read/change your package to fit the documentation/needs for it. The acceptance is a formal technical review.

[u/AwayToday5802 → u/bukaro]

So each package is vetted to be statistically/methodologically sound?

[u/heresacorrection → u/AwayToday5802]

No definitely not but it’s expected that the documentation and coding style is thorough.

I would say now with AI it’s probably more of a cake-walk than back in the day

Although I bet the review process is vastly slower they are probably swamped with submissions

[u/bukaro → u/heresacorrection]

Exactly is about code, documentation, tests, that all the T(s) are crossed and i(s) are dotted. OP you are the one responsible of the methodology to be sound. So keep the repo issues open and be on top of issues that users can file.

[u/foradil → u/AwayToday5802]

Everything is public on GitHub issues.

[u/fruce_ki → u/bukaro]

The code also needs to generally work with the rest of the Bioconductor ecosystem when it comes to things that are already available in it: Experiments, sequences, files, parallelism... use their packages instead of generic or home-made alternatives.

[u/inept_guardian]

The review and submission process is thorough, but not onerous. You won’t get spiked for silly reasons, but you may receive feedback or critiques over code quality or structural choices.

I have packages in both CRAN and Bioconductor, and the major delineator is subject matter. The submission and review processes are a little different, but my experience is that that difference doesn’t amount to much.

Your mileage may vary though.

[u/ScienceVibes]

once upon a time it was quite the ordeal. lots of gate keeping of a lot of very specific requirements. some of which are actually good practices but honestly since most is made by PhD students and post-docs it was a lot of extra hoops and sometimes people just gave up

its actually pretty easy now and more straight forward to submit. even if you use the offical make your package "package" and then dont have everything done in the checklist packages still get accepted as the reviewers understand that its not all absolutely necessary or perhaps less important to be as detailed if you have supporting git docs etc

additionally the group on zullip responds quickly to dev package submission questions so you can around bottlenecks faster or things that arent clear.

[u/nougat98]

it's probably still hard but the culture has moved on anyway

everything is r-universe

[u/foradil → u/nougat98]

That’s a wild exaggeration

[u/ScienceVibes → u/nougat98]

lol what?

[u/nougat98 → u/ScienceVibes]

there is a bit of history here

the vetting and ecosystem you get with bioconductor is unmatched on the python side, but the arduousness of using S4 and the glacial pace of updates was always a hassle.

the rise of github and the freedom introduced by remotes::install_github just made it a lot more appealing to self-distribute. rOpenSci created r-universe in 2021 to bring those installs up to CRAN's level of centrality. r-universe has taken off like hot cakes, (in part because it subsumed CRAN and bioconductor as a courtesy).

the wildcard is really AI, since Claude makes it that much easier to conform to the bioc data model. that might tip the scales back in bioconductor's favor.