[Bioc-devel] Submit data package or use AnnotationHub?

Shepherd, Lori Lori.Shepherd at RoswellPark.org
Fri Dec 22 16:43:38 CET 2017

The choice to use AnnotationHub vs leaving the data in your package is a personal choice.

We encourage the use of the hubs as it has the potential to reach a broader audience and separates functions from data, keeping packages light weight. The hubs also provide others an opportunity to work with the annotations independent of your package. But the decision is yours.

If you would like to proceed with using the Hubs I can assist you.  We would give you temporary access to a temporary directory to upload data. We will move it to the appropriate location on S3. We suggest having subdirectories for versioning if you anticipate the files being updated in the future.  In order to put the data into production on the hubs we would need the packages to have the properly formatted metadata.csv.  Additional information for annotation packages that use the hub can be found here:


The metadata.csv file can be tested for proper format by using AnnotationHubData::makeAnnotationHubMetadata  function



If you would like to proceed this rout please email me at lori.shepherd at roswellpark.org for access credentials.

Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

From: Bioc-devel <bioc-devel-bounces at r-project.org> on behalf of Steve Lianoglou <mailinglist.honeypot at gmail.com>
Sent: Thursday, December 21, 2017 3:26:48 PM
To: bioc-devel at r-project.org
Subject: [Bioc-devel] Submit data package or use AnnotationHub?

Hi all,


I'm looking to get guidance on how to handle data packages that
support a suite of software packages I'd like to submit to

More Detail:

We (Genentech) have opened sourced some packages I've been developing
internally for the past few years that facilitate the execution and
exploration of gene set enrichment analyses.


I will submit them to bioc "in the normal way", however my question is
how I should do that because there are also data packages I have (that
are Suggest(ed) by multiGSEA) that need to go in as well.

Would these data go in as data packages or via AnnotationHub?

multiGSEA provides convenience wrappers to retrieve genesets from
different sources. One of these resources is the gene set collections
made available by MSigDB. Using multiGSEA, a user can get the hallmark
and c2 gene set collections like so:

gdb.human <- getMSigGeneSetDb(c("h", "c2"), "human")
gdb.mouse <- getMSigGeneSetDb(c("h", "c2"), "mouse")

These function calls check if the following data packages are
installed and retrieve the appropriate gene sets if so (otherwise they
raise an error):


I've created these data packages so that they approximate what I think
looks like something suitable for AnnotationHub (ie. with working
inst/scripts/make-data.R scripts). These data packages start with
MSigDB's gene set *xml files (ie. 'msigdb_v6.1.xml') and convert them
into multiGSEA::GeneSetDb *.rds objects which are then used by the
multiGSEA and multiGSEA.shiny packages.

I'm curious how to proceed from here?


ps: I know bioc looks down on not using "foundational" bioc classes,
so we can have this discussion during pkg review, but a GeneSetDb
object is a reimagined take on the GSEABase::GeneSetCollection.
Unfortunately the latter just wasn't providing the functionality I
wanted for how I felt like I wanted to interact with collections of
genesets ... mulitGSEA provides methods to convert a GeneSetCollection
to a GeneSetDb, and vice versa

Steve Lianoglou
Bioinformatics Scientist
Cancer Immunology

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