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
Hi Leonardo,
Keep in mind that GitHub and the Bioconductor git server are two
different animals.
You should be pushing your changes to the git server as you would with
software
packages ( `g...@git.bioconductor.org:packages/derfinderData` ).
My guess is that the hook is looking at the version
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:
>
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
(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
Hi,
thanks for the answers.
Since we only use 5 functions from the package within one function in our
package, I hoped to get around it by masking this function in a special way.
The package is not dependent on PEER and works without it perfectly. Its just
to make it easier for the user if
Forgot to mention that here's how news() select which file to parse if
there are several:
## Look for new-style inst/NEWS.Rd installed as NEWS.Rd
## If not found, look for NEWS.md.
## If not found, look at old-style
## NEWS inst/NEWS
## installed as NEWS (and ignore ChangeLog files).
Source:
Note that in R-devel, we have that
(https://cran.r-project.org/doc/manuals/r-devel/NEWS.html):
* news() gains support for ‘NEWS.md’ files.
That is, news(package = pkg) not only finds NEWS.md (as before) but
also parses it (into sections etc.) analogously to how it parses
NEWS.Rd and NEWS.
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
Dear all,
My experience (and things may have changed since I set this up) is that
NEWS and NEWS.md serve different purposes despite a very similar
syntax. The former is used by news() and displayed on the Bioconductor
page (would NEWS.md be used if NEWS was absent?), while the one with the
md
hi,
it seems that the PEER repository hasn't been updated in the last 7
years and that the package is distributed under a GPL-2 license. if i'm
interpreting this correctly, you could copy that code into your
package redistributing it under the GPL-2 license and asking the users
of PEER to
It is a major weakness of PEER that it has not been submitted to a standard
repository. Of course, that is up to the PEER developers, but the community
should put pressure on them.
On Tue, Sep 25, 2018 at 12:40 PM Christian Mertes wrote:
> Hi all,
>
> Im the developer of OUTRIDER. Our package
Hi all,
Im the developer of OUTRIDER. Our package normalises RNA-seq count data and
finds expression outliers within the population.
During the development we compared our approach against PCA and PEER. The later
one is a well established method to normalise RNA-seq data.
It can be used currently. If you remove the .md extension but keep the format
in should be recognized. As described in the ?news help page
If 'package' is '"R"' (default), a news db is built with the news
since the 3.0.0 release of R (corresponding to R's top-level
'NEWS'
Dear Bioconductor team,
I found that the new R version 3.5.1, to be used with the new release of
Bioconductor, supports the ‘NEWS.md’ files.
I updated my package (BioCor) to use `NEWS.md`. However, on the devel
landing page of the package stills shows the old file NEWS file. This is
consistent
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