For 10X experiments, the Bioc-devel version of DropletUtils will read in
the additional features as extra rows in the count matrix. This reflects
how they are stored in the 10X output format. The row metadata will
record the nature of the feature.
In some cases it may be desirable to keep all the
Hi Steve,
Pretty sure MultiAssayExperiment, containing SingleCellExperiments,
would fit the bill, but I'm not familiar with those data types.
Michael
On Tue, Jan 22, 2019 at 2:18 PM Steve Lianoglou
wrote:
>
> Comrades,
>
> Sorry if I'm out of the loop and have missed anything obvious.
>
> I was
Comrades,
Sorry if I'm out of the loop and have missed anything obvious.
I was curious what the plans are in the single-cell bioconductor-verse
to support single cell experiments that produce counts from different
feature-spaces, such as those produced by CITE-seq / REAP-seq, for
instance.
In th
During this week we will be updating the Single Package Builder to use a new
MAC builder. During this updating and testing, the Single Package Builder may
produce some sporadic ERRORs or experience intermittent periods of downtime.
We will be as quick as possible and hope to keep the interru
You could see if there is any existing data already in Bioconductor for use
with your package. That would be preferable.
http://bioconductor.org/packages/release/BiocViews.html#___Software
searching for fastq - you could see what data ShortRead, seqTools, and
FastqCleaner
similarly you cou
Hi,
I have changed the email address associated with that account. Please login to
the BiocCredentials app and add your SSH keys. You should be able to gain
access to the Git repository then.
https://git.bioconductor.org/BiocCredentials
You’d first need to activate your account.
Best,
Nitesh
Hi everyone,
I am currently working on a R package called BgeeCall allowing to
automatically generate present/absent expression calls from any RNA-Seq
fastq files as long as the species is present in Bgee (https://bgee.org/)
.
The package is almost ready and I am currently writing the vignette and
require is expensive and detach() fraught with subtle difficulties. Using
withCallingHandlers is more elegant than capture.output(). See and direct
further commentary to the issue.
Martin
On 1/22/19, 4:41 AM, "Bioc-devel on behalf of Levi Waldron"
wrote:
BTW I just noticed the alternat
BTW I just noticed the alternative approach of searching through the
warnings, used at
https://github.com/Bioconductor/bioc_docker/blob/5be6d37ded4f97995640cbb3a7d201165234b1e4/src/core/install.R.in#L42
:
if (!is.null(warnings()))
{
w <- capture.output(warnings())
if (length(grep("is not a
I opened an issue on BiocManager (
https://github.com/Bioconductor/BiocManager/issues/39) somewhat related to
Sean's recent post, about what BiocManager::install() should return, and it
occurs to me that I should mention it here too for feedback:
> Having `BiocManager::install()` return the "pkgs"
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