Thank you all for the feedback. Just to give some extra context, here we have
the Python and Javascript versions of the biothings_client:
https://github.com/biothings/biothings_client.py
https://github.com/biothings/biothings_client.js
And here is the work-in-progress R client:
https://git
API discoverability is a big problem in languages with a functional syntax.
Namespaces are verbose, but they do provide for constrained autocompletion.
Prefixing all symbols with an abbreviation like "bt_" seems too adhoc to
me, but it is common practice. Explicitly querying for methods takes the
u
Hi Nitesh,
Thanks for the quick reply -- after reading through the exchanges on the list
over the past week, I realized that my problem was related to the fact that my
SSH keys were named github_rsa and github_rsa.pub (rather than id_rsa and
id_rsa.pub). I added a config file (as suggested by t
On 10/19/2017 09:24 PM, Charles Plessy wrote:
(Just sharing my thoughts as those days I am spending quite
some time preparing the upgrade of a Bioconductor package).
Le Fri, Oct 20, 2017 at 12:50:48AM +, Ryan Thompson a écrit :
gene_client <- BioThingsClient("gene")
query("CDK2", client=ge
Thanks for those additional comments, Levi. I don't think you were being
unfair to phyloseq, and it sounds like some of the issues involved are
still relevant (e.g. new domain, new contributor).
I wanted to riff on Martin's comment about "incremental gain rather than
perfection". I imagine there a
On Thu, Oct 19, 2017 at 5:25 PM, Chunlei Wu wrote:
> Hello BioC-dev group,
>
>
>We are working on a new R package right now and plan to submit
> it to Bioconductor soon. It's a unified R client for the collection of
> BioThings APIs (http://biothings.io). Using R6 class, it makes a l
Hi Nitesh
I've re-implemented the latest changes with no duplicate commits and
deprecated the problematic branch.
Again, many thanks for your help.
Regards
Matthew Myint
Life Science Undergraduate, Year 4
NUS
On Wed, Oct 18, 2017 at 9:40 PM, Turaga, Nitesh
wrote:
> Hi Matthew,
>
> I’ve reset y
(Just sharing my thoughts as those days I am spending quite
some time preparing the upgrade of a Bioconductor package).
Le Fri, Oct 20, 2017 at 12:50:48AM +, Ryan Thompson a écrit :
>
> gene_client <- BioThingsClient("gene")
> query("CDK2", client=gene_client)
In addition, since the piping o
The Biothings service looks interesting -- I had a look at the variant
API and noticed that GRASP information is returned. We don't have that
in a convenient form. However we do have plenty of variant and gene
annotation and object classes that are relevant to these.
We have had a discussion lat
Hi Chunlei,
One thing you could do to make the interface more traditional is to have a
global "query" function that takes a client object as an additional
argument.
Usage would be something like:
gene_client <- BioThingsClient("gene")
query("CDK2", client=gene_client)
To simplify this for commo
Hello BioC-dev group,
We are working on a new R package right now and plan to submit it to
Bioconductor soon. It's a unified R client for the collection of BioThings
APIs (http://biothings.io). Using R6 class, it makes a lot sense to me as I'm
coming from Python's OOP experience. I
On 10/19/2017 06:21 AM, Moritz Gerstung wrote:
Hi all
It looks like a number of packages have failed the latest Windows build due to
Vignette/MikTeX issues.
'a number' is pretty good -- there were almost 1000 failures in
Wednesday's build report! Back closer to normal now...
Martin
The
On 10/19/2017 03:10 PM, Laurent Gatto wrote:
On 19 October 2017 13:22, Shepherd, Lori wrote:
Hello Bioconductor,
We have added DOI's for packages on Bioconductor package landing
pages. The DOI will get generated automatically when a package is
accepted to Bioconductor. This is the recommended
Many Thanks to Sean Davis for coming up with how to generate and providing the
infastructure!
Lori Shepherd
Bioconductor Core Team
Roswell Park Cancer Institute
Department of Biostatistics & Bioinformatics
Elm & Carlton Streets
Buffalo, New York 14263
From:
On 19 October 2017 13:22, Shepherd, Lori wrote:
> Hello Bioconductor,
>
> We have added DOI's for packages on Bioconductor package landing
> pages. The DOI will get generated automatically when a package is
> accepted to Bioconductor. This is the recommended reference to use for
> publication/cit
On 10/19/2017 10:12 AM, Levi Waldron wrote:
Thanks for all your thoughts Joey, and I hope I didn't come across as
critical of phyloseq in particular. In fact, the couple packages I created
as a post-doc (doppelgangR and ffpe) did exactly the same thing, but unlike
phyloseq have never been used en
On 10/19/2017 11:06 AM, Vincent Carey wrote:
On Thu, Oct 19, 2017 at 10:12 AM, Levi Waldron
wrote:
Thanks for all your thoughts Joey, and I hope I didn't come across as
...
On Wed, Oct 18, 2017 at 11:36 PM, Paul Joseph McMurdie
wrote:
...
- There actually *still isn't core support for evo
There may be a common pattern emerging where derivatives of
SummarizedExperiment add support for specific feature types. Currently, we
have ranges, and it was suggested in a package submission thread to support
gene sets (or pathways, etc). Those could also be represented by a graph,
or something m
On Thu, Oct 19, 2017 at 10:12 AM, Levi Waldron
wrote:
> Thanks for all your thoughts Joey, and I hope I didn't come across as
> ...
>
> On Wed, Oct 18, 2017 at 11:36 PM, Paul Joseph McMurdie
> wrote:
>
> ...
>
> > - There actually *still isn't core support for evolutionary trees in
> BioC* (as
>
And/or
MAE : SE :: Ragged : Tidy
;-)
--t
On Thu, Oct 19, 2017 at 10:27 AM, Tim Triche, Jr.
wrote:
> MAE : SE :: Tensor : Matrix
>
> --t
>
> On Thu, Oct 19, 2017 at 10:16 AM, Levi Waldron <
> lwaldron.resea...@gmail.com> wrote:
>
>> On Wed, Oct 18, 2017 at 8:00 PM, Dario Strbenac <
>> dstr7..
MAE : SE :: Tensor : Matrix
--t
On Thu, Oct 19, 2017 at 10:16 AM, Levi Waldron
wrote:
> On Wed, Oct 18, 2017 at 8:00 PM, Dario Strbenac <
> dstr7...@uni.sydney.edu.au>
> wrote:
>
> > Good day,
> >
> > It might be useful to readers to have a comparison table (ticks and
> > crosses) in the MultiA
On Wed, Oct 18, 2017 at 8:00 PM, Dario Strbenac
wrote:
> Good day,
>
> It might be useful to readers to have a comparison table (ticks and
> crosses) in the MultiAssayExperiment vignette that compares the features
> available in it to those available in SummarizedExperiment, to allow
> quicker de
Thanks for all your thoughts Joey, and I hope I didn't come across as
critical of phyloseq in particular. In fact, the couple packages I created
as a post-doc (doppelgangR and ffpe) did exactly the same thing, but unlike
phyloseq have never been used enough for it to make much difference :).
This c
Hello Bioconductor,
We have added DOI's for packages on Bioconductor package landing pages. The DOI
will get generated automatically when a package is accepted to Bioconductor.
This is the recommended reference to use for publication/citations/etc. The
DOI link should automatically redirect to
confirmed, thanks!
On 19/10/2017 12:09, Martin Morgan wrote:
On 10/19/2017 07:04 AM, jmason wrote:
Hi bioc-devel,
I am maintainer of the IMPCdata package. I can clone the package, but
when I push I get:
➜ IMPCdata git:(master) ✗ git push
FATAL: W any packages/IMPCdata jmason DENIED by fa
On 10/19/2017 07:04 AM, jmason wrote:
Hi bioc-devel,
I am maintainer of the IMPCdata package. I can clone the package, but
when I push I get:
➜ IMPCdata git:(master) ✗ git push
FATAL: W any packages/IMPCdata jmason DENIED by fallthru
(or you mis-spelled the reponame)
fatal: Could not read
Hi bioc-devel,
I am maintainer of the IMPCdata package. I can clone the package, but
when I push I get:
➜ IMPCdata git:(master) ✗ git push
FATAL: W any packages/IMPCdata jmason DENIED by fallthru
(or you mis-spelled the reponame)
fatal: Could not read from remote repository.
Please make su
Thanks, Levi, nice slides.
In case it is a helpful perspective, I'll try to share what I recall of my
thought process as author of phyloseq. And I should preface by admitting
that I've been embarrassed by this major development oversight for some
years now.
At the beginning of 2011 I was a new po
Hi all
It looks like a number of packages have failed the latest Windows build due to
Vignette/MikTeX issues.
The common denominator appears to be
> Warning: running command
> '"C:\PROGRA˜1\MIKTEX˜1.9\miktex\bin\x64\texify.exe" .. had status 1
> Error in find_vignette_product(name, by = "tex
I just converted my gene set data structures to GSEABase::GenSet
class. I think that one major advantage is that I just transferred the
burden of staying up to date with gene set formats to people working
specifically on that. If the file formats from the MSigDB change,
someone will work on updatin
Dear developers,
I have stumbled upon issues with our package vignette. In the windows build:
* creating vignettes ...Warning: running command
'"C:/Users/biocbuild/bbs-3.6-bioc/R/bin/x64/Rscript" --vanilla
--default-packages= -e "tools::buildVignettes(dir = '.', tangle =
TRUE)"' had status
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