with it (to
raise awareness of the issue). Perhaps some changes are needed in the
build system to avoid this issue moving forward.
All the best,
Bohdan
--
Bohdan Khomtchouk, Ph.D.
AHA Postdoctoral Fellow, Gozani & Assimes Labs
Department of Biology & Department of Medicine
Division of Cardio
in order
for the /devel landing page to update itself?
Note: the /devel landing page says v.1.7.2 and I pushed v.1.7.2. Perhaps
this is a mistake and I should have pushed v.1.7.3 in order for the changes
to be reflected?
--
Bohdan Khomtchouk, Ph.D.
AHA Postdoctoral Fellow, Gozani & Assimes
us/Mus...
# $sourcesize: 29183870
# $tags: c("GTF", "ensembl", "Gene", "Transcript", "Annotation")
# retrieve record with 'object[["AH63797"]]'
On Wed, Sep 26, 2018 at 2:01 PM Martin Morgan
wrote:
> maybe you are not using the 'devel' ve
2018 at 3:48 PM, Bohdan Khomtchouk <
> khomtchouk...@gmail.com> wrote:
>
>> Martin, I don't see it unfortunately:
>>
>> > query(hub, "Mus_musculus.GRCm38.93.chr.gtf")
>> AnnotationHub with 0 records
>> # snapshotDate(): 2018-04-30
>&g
= hub[["AH63797"]]
>
> Need the path rather than the imported path? use cache(hub["AH63797"])
> instead.
>
> Martin
>
> On 09/25/2018 09:59 PM, Bohdan Khomtchouk wrote:
> > To generate mouse.rda, I used:
> >
> > library(rtracklayer)
> >
To generate mouse.rda, I used:
library(rtracklayer)
mouse <- readGFF("
ftp://ftp.ensembl.org/pub/release-93/gtf/mus_musculus/Mus_musculus.GRCm38.93.chr.gtf.gz
")
And then I saved the object as mouse.rda
On Tue, Sep 25, 2018 at 6:33 PM Bohdan Khomtchouk
wrote:
> Her
Here it is:
https://github.com/Bohdan-Khomtchouk/geneXtendeR/blob/master/data/mouse.rda
On Tue, Sep 25, 2018 at 6:23 PM Vincent Carey
wrote:
> (resending with reply all -- please reply to this one)
>
> Can you say some more about the content of the file? Perhaps it can be
deR'
--
Bohdan Khomtchouk, Ph.D.
AHA Postdoctoral Fellow, Gozani & Assimes Labs
Department of Biology & Department of Medicine
Division of Cardiovascular Medicine
Stanford University
Stanford, CA 94305
https://profiles.stanford.edu/bohdan-khomtchouk
CONFIDENTIALITY NOTICE: Informatio
st"
## [15] "variable" "variable_description"
## [17] "contact" "supplementary_file"
Clearly, there should also be an "Organism" metadata field, e.g.:
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4032
Please a
ium=email_sig_campaign=gmail_api_content=thumb>
Bohdan Khomtchouk
about.me/bohdankhomtchouk
<https://about.me/bohdankhomtchouk?promo=email_sig_source=product_medium=email_sig_campaign=gmail_api_content=thumb>
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