On Mon, Jan 7, 2019 at 3:26 PM Henrik Bengtsson
wrote:
>
> 1. To achieve fully numerically reproducible RNGs in way that is
> *invariant to the number of workers* (amount of chunking), I think the
> only solution is to pregenerated RNG seeds (using
> parallel::nextRNGStream()) for each individual
I don't know if this is helpful for BiocParallel, but there's an extension
for the foreach package that ensures reproducible RNG behavior for all
parallel backends: https://cran.r-project.org/web/packages/doRNG/index.html
Perhaps some of the principles from that package can be re-used?
On Mon, Ja
Hi Robert,
My understanding is that the "requireNamespace" trick, combined with
listing the package in "Suggests" is the standard way to implement optional
dependencies. Users of limma that never use duplicateCorrelation or other
functions that require statmod will never need to install it.
For m
Hi Martin,
Is the intent that the BiocManager package should never be loaded via
library, but functions in the package should always be called as
BiocManager::FUN()? If not, I would consider prefixing the functions with
"bioc".
Also, I assume that once this BiocManager package is on CRAN, the
bio
ons/BiocFileCache/citation.html>
?
Regards,
Ryan Thompson
On Tue, Apr 17, 2018 at 12:23 PM Ryan Thompson wrote:
> I wasn't specific about what I meant by "structured" because I'm not
> certain what kind of citation data types CiteAs can handle, though I'd
> assume bibt
file. The best way to programmatically
> get these at the moment
> is through the git repository via:
>
> git archive
> --remote=g...@git.bioconductor.org:packages/MultiAssayExperiment.git \
>HEAD inst/CITATION | tar -xO inst/CITATION > citation.txt
>
> although, we wou
hich isn't really an option for a web service like
this, which wants to return a result quickly. Does anyone know a good way
to access this info?
Thanks,
Ryan Thompson
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Bioc-devel@r-proje
t the need for separate installation of other command-line tools.
Regards,
Ryan Thompson
On Sun, Nov 12, 2017 at 2:12 PM Ioannis Vardaxis
wrote:
> Hi,
> I have developed a package and is current under review from
> Bioconductor. In the future I am considering of making some chang
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
I think the main reason for reusing/subclassing core classes that users can
appreciate is that it makes it much easier for users to integrate multiple
packages into a single workflow. Only the most basic of pipelines uses just
a single Bioconductor package. For instance, an "edgeR" pipeline obvious
Hi Aaron,
I'm making a ChIP-Seq analyisis pipeline using csaw, and I'm running into
an inconsistent error/segfault. I've reduced it to a test case which you
can find here:
https://www.dropbox.com/sh/2a2vpb5ek4413fx/AAAXwCaTzsAmfyPefwAbFg8Na?dl=0
The test case consists of my R workspace saved with
They wouldn't be exactly consistent even if they used the same prior count,
since the calculations are not identical. edgeR normalizes the prior count
by each library's normalization factor so that log fold changes are always
squeezed toward zero, while voom, if I understand correctly, does not
nor
Actually, the code looks like it should be adding these names, so I need to
go back through my code and get back to you on that issue.
On Jul 7, 2015 9:58 AM, "Ryan C. Thompson" wrote:
> I've also encoundered another problem, this time I believe related to a
> change the the frma package which re
It looks like dplyr has support for base R lists as columns in data frames:
http://cran.r-project.org/web/packages/dplyr/vignettes/data_frames.html
Hopefully that feature is flexible enough to accommodate anything that
looks sufficiently like a vector. Is love to give this a try, but I can't
find
t; which gives a useless
>> result.
>> seqinfo(fll)
>>
>> ## Now add a method
>> setMethod("seqinfo", signature=list(x="BamFileList"), function (x)
>> {
>> Reduce(merge, lapply(x, seqinfo))
>> }
>> )
>>
>&
Thanks! I patched my local copy on my own, so I'll be fine until the next
release.
On Mar 25, 2014 3:04 AM, "Julian Gehring" wrote:
> Hi Ryan,
>
> Thank you for the detailed bug report and already providing a fix for
> this. I have added your patch to 'les_1.13.2' and pushed it to
> bioc-devel,
The code that I wrote intentionally avoids checking for package variables,
since I consider that a separate problem. Package variables can be provided
to the child by leading the package, whereas user-defined variables must be
serialized in the parent and sent to the child.
I think I could fairly
Couldn't one test for existence by trying to open the BamFile object, and
possibly read one sequence (or maybe just read the header since I guess a
valid bam file can contain zero sequences)?
On Jan 7, 2013 1:32 PM, "Henrik Bengtsson" wrote:
> On Mon, Jan 7, 2013 at 12:32 PM, Nicolas Delhomme
>
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