[Bioc-devel] New annotation hub package?

[Kern, Lori]

I can assist you with this request.   In the future there is the email hubs using bioconductor.org for these types of requests instead of the developer mailing list as mentioned in the documentation.

I'll contact you off mailing list for further details and instruction.

Cheers,


Lori Shepherd - Kern

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________
From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Sara López Ruiz de Vargas <lopez_s using molgen.mpg.de>
Sent: Wednesday, April 24, 2024 9:17 AM
To: bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: [Bioc-devel] New annotation hub package?

Dear developers community,

We are currently developing a package for which we are quite sure we
will need a supporting AnnotationHub or ExperimentHub package to go with
it.
We are using a set of gene annotations (GENCODE version 40 hg38) and
enhancer annotations (ENCODE registry of cCREs v3), which are not
available in the AnnotationHub.
Correct me if I’m wrong.

On top of that, our package depends on in house precomputed datasets
that occupy a lot of space.
We have solved this issue temporarily by making the annotations and the
precomputed data into RSQLite databases which the user can download
(into inst/extada)
once the package is installed. This however makes the inst/extdata
folder really large (above 5GB). Most likely a Hub package would be a
better solution.

When looking at the documentation (
https://secure-web.cisco.com/1SsSYiZvjhKsQTFDCiJs0zb6X29DjrpzlJ2hbWrRlx8i-tJpOM_X_CeJJbTIno7lpn5KpG38T0R-RtgcpXEhht9UGyKnVc-Xhzfc7uJKGpjgkNWPgaAqEkv7dtSBqHZjisJHne-FoHtc3puPdivFQ5JoxHenR3tMndo8F4AxdcaDrmc86qyiC7wulOGvXG8urAj43FaLkpCC-GQSWFFCeqaN6Bj55ech4IoyaCMU0cfKv70FAKXhk1dTjtQjDe9e8SxKEhdSipEWpUWIsk-QnozRWMFNRit5mLBhjgQzTW60FMWumv_ztFHv9Zhl1YhgZ/https%3A%2F%2Fbioconductor.org%2Fpackages%2Fdevel%2Fbioc%2Fvignettes%2FHubPub%2Finst%2Fdoc%2FCreateAHubPackage.html
) one of the first things
mentioned is to contact a Bioconductor team member. I was wondering if I
could find someone in this forum who could help with this.

Best regards,

Sara Lopez

--
Sara López Ruiz de Vargas
Max Planck Institute for Molecular Genetics
Vingron Lab / Dept. of Computational Molecular Biology
Ihnestraße 63-⁠73
14195 Berlin
GERMANY

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