Looks like that was the issue, thanks Vincent & Martin!
> hub = AnnotationHub()
snapshotDate(): 2018-08-20
> isDevel()
[1] TRUE
> query(hub, "Mus_musculus.GRCm38.93.chr.gtf")
AnnotationHub with 1 record
# snapshotDate(): 2018-08-20
# names(): AH63797
# $dataprovider: Ensembl
# $species: Mus muscu
maybe you are not using the 'devel' version of Bioconductor?
On 09/26/2018 03:48 PM, Bohdan Khomtchouk wrote:
Martin, I don't see it unfortunately:
> query(hub, "Mus_musculus.GRCm38.93.chr.gtf")
AnnotationHub with 0 records
# snapshotDate(): 2018-04-30
But perhaps it needs to be added to Anno
Just did, same result:
> hub = AnnotationHub()
snapshotDate(): 2018-04-30
I re-installed AnnotationHub package as well.
On Wed, Sep 26, 2018 at 1:16 PM Vincent Carey
wrote:
> your annotation hub is out of date. run hub = AnnotationHub() and try
> again
>
> On Wed, Sep 26, 2018 at 3:48 PM, Bo
your annotation hub is out of date. run hub = AnnotationHub() and try again
On Wed, Sep 26, 2018 at 3:48 PM, Bohdan Khomtchouk
wrote:
> Martin, I don't see it unfortunately:
>
> > query(hub, "Mus_musculus.GRCm38.93.chr.gtf")
> AnnotationHub with 0 records
> # snapshotDate(): 2018-04-30
>
> But
Martin, I don't see it unfortunately:
> query(hub, "Mus_musculus.GRCm38.93.chr.gtf")
AnnotationHub with 0 records
# snapshotDate(): 2018-04-30
But perhaps it needs to be added to AnnotationHub, because I see other
.chr.gtf files that go up to 86 (while I'm using 93 in this original post):
> quer
hmm, does it make sense to submit the hg19, hg38, and mm10 HMM CpG island
predictions to AnnotationHub?
R> qhs <- query(ah, "island" )
R> qhs
AnnotationHub with 4 records
# snapshotDate(): 2018-08-20
# $dataprovider: UCSC
# $species: Homo sapiens
# $rdataclass: GRanges
# additional mcols(): taxono
Good news, the file is in AnnotationHub and can be used from there.
There is a download cost the first time but not subsequently.
library(AnnotationHub)
hub = AnnotationHub()
query(hub, "Mus_musculus.GRCm38.93.chr.gtf.gz")
## note 'AH' number, then...
gtf = hub[["AH63797"]]
Need the path rathe
To generate mouse.rda, I used:
library(rtracklayer)
mouse <- readGFF("
ftp://ftp.ensembl.org/pub/release-93/gtf/mus_musculus/Mus_musculus.GRCm38.93.chr.gtf.gz
")
And then I saved the object as mouse.rda
On Tue, Sep 25, 2018 at 6:33 PM Bohdan Khomtchouk
wrote:
> Here it is:
> https://github.co
Here it is:
https://github.com/Bohdan-Khomtchouk/geneXtendeR/blob/master/data/mouse.rda
On Tue, Sep 25, 2018 at 6:23 PM Vincent Carey
wrote:
> (resending with reply all -- please reply to this one)
>
> Can you say some more about the content of the file? Perhaps it can be
> placed in Experimen
(resending with reply all -- please reply to this one)
Can you say some more about the content of the file? Perhaps it can be
placed in ExperimentHub. "mouse.rda" is not very descriptive. is it
in your github repo?
On Tue, Sep 25, 2018 at 6:25 PM, Bohdan Khomtchouk
wrote:
> I need to includ
I need to include an important .rda file in the /data folder of my
Bioconductor package. However, this .rda file exceeds 5 Mb in size. Do I
have any other options besides for deleting it?
bohdankhomtchouk$ git push origin master
Counting objects: 65, done.
Delta compression using up to 8 threa
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