[Bioc-devel] AnnotationHub (2)

Shepherd, Lori Lori.Shepherd at RoswellPark.org
Tue Mar 27 18:23:25 CEST 2018

It is still a work in progress.  For now the old-style is still active and encouraged to use.  We would recommend making an Annotation Package that utilizes AnnotaitonHub


We will keep in mind the request to add annotation specific metadata as we continue to develop the next generation hub.

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 Kasper Daniel Hansen <kasperdanielhansen at gmail.com>
Sent: Tuesday, March 27, 2018 5:16:34 AM
To: bioc-devel at r-project.org
Subject: [Bioc-devel] AnnotationHub (2)

What is the current state for AnnotationHub (2)? I have recently figured
out (read: pestered the people who knows the arcane incantations for this
resource; I have been taught the sacred rituals) the interface to the
encode data portal and we should make an AnnotationHub interface to this.
But should this be old-style or new?

Also, this has uncovered a table of structured metadata for the resource,
essentially a spreadsheet with organized columns.  It seems very relevant
for users to get access to the data in this spreadsheet, which would
essentially be a resource dependent data.frame. I don't think this is
supported by the classic AnnotationHub, but I very much think this should
be supported in the future.  One could also envision resource and
dataset-dependent information such as the phenotypes in GEO for a fixed


        [[alternative HTML version deleted]]

Bioc-devel at r-project.org mailing list

This email message may contain legally privileged and/or confidential information.  If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited.  If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you.
	[[alternative HTML version deleted]]

More information about the Bioc-devel mailing list