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 experiment. Best, Kasper
[Bioc-devel] AnnotationHub (2)
3 messages · Kasper Daniel Hansen, Shepherd, Lori, Vincent Carey
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 https://bioconductor.org/packages/release/bioc/vignettes/AnnotationHub/inst/doc/CreateAnAnnotationPackage.html 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)
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
experiment.
Best,
Kasper
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can you pass along some of the magic kasper? what encode portal are you talking about? On Tue, Mar 27, 2018 at 5:16 AM, Kasper Daniel Hansen <
kasperdanielhansen at gmail.com> wrote:
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
experiment.
Best,
Kasper
[[alternative HTML version deleted]]
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