(dev=pdf, fig.align=center, cache=FALSE,
message=FALSE, out.width=.55\\textwidth, echo=TRUE,
results=markup, fig.show=hold)
options(width=60)
@
Am I missing something?
Best,
davide
--
Davide Risso, PhD
Post Doctoral Scholar
Department of Statistics
University of California, Berkeley
344 Li Ka
]]
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--
Davide Risso, PhD
Post Doctoral Scholar
Department of Statistics
University of California, Berkeley
344 Li Ka Shing Center, #3370
Berkeley, CA 94720-3370
E-mail: davide.ri...@berkeley.edu
On Wed, Sep 10, 2014 at 11:19 AM, Martin Morgan mtmor...@fhcrc.org wrote:
On 09/10/2014 10:39 AM, davide risso wrote:
I just wanted to add my support to Josef request.
During the last few weeks I received several emails from users asking
me if I plan to make a version of RUVSeq compatible with R
'development version'
flags on the page.
Yes. I also think they follow the link and just copy/paste the
biocLite() command without reading the rest of the page.
Best,
davide
On Wed, Sep 10, 2014 at 12:21 PM, Martin Morgan mtmor...@fhcrc.org wrote:
On 09/10/2014 11:37 AM, davide risso wrote:
Thanks
Hi all,
I don't know why but this is not working for me.
I deleted the bridge for my RUVSeq package.
I forked Bioconductor-mirror/RUVSeq into drisso/RUVSeq-mirror
I then run:
$ git clone https://github.com/drisso/RUVSeq-mirror
$ bash ../update_remotes.sh
$ git checkout devel
error: pathspec
-
From: davide risso risso.dav...@gmail.com
To: Leonardo Collado Torres lcoll...@jhu.edu, Dan Tenenbaum
dtene...@fredhutch.org, Jim Hester
james.f.hes...@gmail.com
Cc: bioc-devel@r-project.org
Sent: Friday, June 19, 2015 8:07:29 PM
Subject: Re: [Bioc-devel] Bioconductor Git/GitHub Mirrors
. I agree
it is not as clean from a design perspective, but you get 100% of the
functionality and you can write a separate checker for the colData argument.
On Thu, Jun 18, 2015 at 2:00 PM, davide risso risso.dav...@gmail.com
wrote:
Thank you all for the responses.
I didn't think about
. That actually solves a problem for me too (I don't
intend to expose nested DataFrames to the users though).
On 6/17/15 7:23 PM, Martin Morgan wrote:
On 06/17/2015 11:41 AM, davide risso wrote:
Dear list,
I'm creating an R package to store RNA-seq data of a somewhat large
Dear list,
I'm creating an R package to store RNA-seq data of a somewhat large project
in which I'm involved.
One of the initial goals is to compare different pre-processing pipelines,
hence I have multiple expression matrices corresponding to the same samples.
The SummarizedExperiment class
Dear Bioc developers,
I recently downloaded three publicly available single-cell RNA-seq datasets
from the NCBI GEO/SRA repository and created an R package with some
gene-level summaries (read counts and FPKMs).
I'm currently using the package locally for my own tests, but I'm thinking
that this
sharing.
Best,
davide
On Thu, Mar 3, 2016 at 12:50 PM Hervé Pagès <hpa...@fredhutch.org> wrote:
> Hi Davide,
>
> On 03/01/2016 02:25 PM, davide risso wrote:
> > Dear Bioc developers,
> >
> > I recently downloaded three publicly available single-cell RNA-seq
>
m
> >> > PH 502-509-1827
> >> >
> >> > To call in the statistician after the experiment is done may be no
> more
> >> > than asking him to perform a post-mortem examination: he may be able
> to say
> >> > what the experiment died of.
Dear list,
we are developing a new package that defines a class that builds on
SummarizedExperiment and also imports the CRAN package phylobase.
The class "Annotated" is defined both in the S4Vectors package (a
dependency of SummarizedExperiment) and in the RNeXML package (a dependency
of
(Class, where, package = package, resolve.msg =
> > resolve.msg)
> >
> > but I haven't quite got to the bottom of that. Also, I think these are
> both
> > different from but related to
> >
> >> suppressPackageStartupMessages(library(Statomica))
ps://travis-ci.org/epurdom/clusterExperiment/builds/126175973
Thanks,
Davide
On Mon, Apr 25, 2016 at 2:00 PM davide risso <risso.dav...@gmail.com> wrote:
> Thank you Michael and Martin for looking into this!
>
> Best,
> davide
>
>
> On Mon, Apr 25, 2016 at 1:49 PM
Hi Michael,
Thanks for looking into this.
Can you or someone with push permission to S4Vectors implement the workaround
that you mentioned?
Happy to create a pull request on Github if that helps.
We’re trying to solve this to fix the clusterExperiment package build on
Bioc-devel.
Thanks,
Hi all,
Can you please give write access to the scRNAseq package to Aaron Lun (
infinite.monkeys.with.keyboa...@gmail.com)?
Best,
Davide
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