LTLA / scRNAseq

Clone of the Bioconductor repository for the scRNAseq package.
http://bioconductor.org/packages/devel/data/experiment/html/scRNAseq.html
24 stars 12 forks source link

introduce pubmed links used for README.md and datasetsPage() function #43

Closed vjcitn closed 9 months ago

vjcitn commented 9 months ago

These enhancements are en route to the establishment of an AnVIL workspace devoted to the package. See https://app.terra.bio/#workspaces/landmarkanvil2/Bioconductor-Package-scRNAseq and scroll down for the hyperlinked table

LTLA commented 9 months ago

Why do these functions need to live here? You could just as easily host them outside of the package, and I don't see how they would be useful to anyone outside of the Anvil use case.

vjcitn commented 9 months ago

Sure, I thought it might be helpful to have a hyperlinked README for the repo, and that the changes to ref.bib were advantageous for helping users get to the associated papers. The functions are there to help users; the reference to AnVIL was just an illustration of additional exposure.

vjcitn commented 9 months ago

https://github.com/vjcitn/scRNAseq#scrnaseq-package is the effect on repo README

LTLA commented 9 months ago

A fleshed-out README is good but I don't think I want to see a hard-coded listing of datasets there, too much of a headache to keep in sync with the assets on ExperimentHub.

I think you might appreciate #42, which switches to the gypsum backend and adds titles, abstracts, PMIDs and other goodies to all datasets. This is available as a SQLite file (see the artifacts here) which can be more readily examined by users without adding all this extra machinery to parse the .bib file.

vjcitn commented 9 months ago

Agreed that getting key metadata out of bibtex is not ideal. What do we have to do to get #42 merged? I will go back to our artifactdb dialogue but any specific steps welcome. Roughly, it sounds like enabling an AnnotationHub-like behavior for client packages in bioconductor, but using artifactdb.

LTLA commented 9 months ago

If we can deal with Bioconductor/Contributions#3280, I will handle the rest of the ETL. The specific plan is to switch all of scRNAseq from ExperimentHub to use gypsum by default in the next release, and then we can have a look at its performance/cost in the wild. Especially if I open it up to third-party contributors who just supply SCEs.

LTLA commented 8 months ago

It is done. Pushed to BioC-devel, let's see how it goes.