> From: Bioc-devel On Behalf Of
> Vincent Carey
> Sent: Sunday, December 10, 2023 1:44 PM
> To: Christian Arnold
> Cc: bioc-devel@r-project.org
> Subject: Re: [Bioc-devel] Missing CHM13v2.0 TxDB and OrgDb objects
>
> Good question. I believe the
Hello, I am working with the new human T2T-CHM13v2.0 assembly and while
a BSgenome package already exists
(BSgenome.Hsapiens.NCBI.T2T.CHM13v2.0), I could not find the
corresponding TxDb and OrgDb packages. Is there any information when
they may also become available so it is easier to work with
For my package SNPhood that did not receive any code changes or updates
in quite a while, I suddenly see errors with Bioc 3.18:
https://master.bioconductor.org/checkResults/3.18/bioc-LATEST/SNPhood/nebbiolo2-buildsrc.html
Error: processing vignette 'workflow.Rmd' failed with diagnostics:
unused
Hi, for a new package submission
(https://github.com/Bioconductor/Contributions/issues/2550), I receive
an automated bot reply with the following:
"The package DESCRIPTION must contain a biocViews field with one or more
valid biocViews terms.
Please fix your DESCRIPTION. See current biocViews
Hi,
it appears that in the newest devel version,
fetchExtendedChromInfoFromUCSC is broken (again). I found an earlier
post here:
https://www.mail-archive.com/bioc-devel@r-project.org/msg06193.html,
which however states that this has been fixed already in the previous
version 1.11.2 of the
Dear Bioconductor developers,
I am having a somewhat mysterious and challenging problem which we
believe is a bug in either (1) BiocParallel or (2) the lpsymphony
library from either Bioconductor or the SYMPHONY backend.
The problem is, in a nutshell, that R silently crashes or, to be more
Dear Bioc-Community,
I was wondering if it is currently possible to only import the first X
reads rather than all reads from an arbitrary BAM file into a list using
Rsamtools with scanBam? I did not find any parameter in scanBamParam
that seems to capture what I need. Specifically, I do not
mation for further
processing.
Do you have any idea if I can save this information more efficiently so
that the overall object size is reduced? I could try an Rle, but the
structure of the data does not be ideal for this...
Any tips are very much appreciated!
Thanks,
Christian
--
e vignette sources from inst/doc
Any help is appreciated, thanks,
Christian
--
—
Christian Arnold, PhD
Staff Bioinformatician
SCB Unit - Computational Biology
Joint appointment Genome Biology
Joint appointment European Bioinformatics Institute (EMBL-EBI)
European Molecul
thin your `setMethod()` call. In particular you do _not_ need to
> write an explicit `@usage` directive.
>
> See
> https://github.com/jimhester/examplePrototype/blob/master/R/package.R
> for an example package without any NOTEs for this situation.
>
> Jim
>
> On Sun, Sep
s is exactly what my function does also...
Thanks,
Christian
--
—
Christian Arnold, PhD
Staff Bioinformatician
SCB Unit - Computational Biology
Joint appointment Genome Biology
Joint appointment European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory (EMBL)
Meye
it behave?
On Thu, May 14, 2015 at 3:35 AM, Christian Arnold
christian.arn...@embl.de mailto:christian.arn...@embl.de wrote:
Hi there,
I am about to develop a Bioconductor package that implements a
custom S4 object, and I am currently thinking about a few issues,
including
Hi there,
I am about to develop a Bioconductor package that implements a custom S4
object, and I am currently thinking about a few issues, including the
following:
Say we have an S4 object that stores a lot of information in different
slots. Assume that it does make sense to extract
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