Hi, Chiagozie.
This list is mainly for developer questions. Your best bet is to ask on
https://support.bioconductor.org/ where you'll get many more eyes on your
question and the broadest possible community will benefit from answers.
When you ask there, consider adding the output of sessionInfo()
Hi, Amin.
You�ll have a more likely chance of an answer if you post to the Bioconductor
support site at https://support.bioconductor.org. This list is really focused
to development-related issues.
Best,
Sean
From: Bioc-devel on behalf of Amin Ali
Date: Monday, October 31, 2022 at 5:18 AM
My sentiments exactly! Great work!
Sean
From: Bioc-devel on behalf of Steve
Lianoglou
Date: Tuesday, September 27, 2022 at 1:25 PM
To: Jennifer Wokaty
Cc: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] Mac ARM64 binaries available
a yeah
thanks for the hard work,
Hi, Pariksheet.
For #1, I suspect that it might be challenging to publish a paper based on the
context you provide, but I do not have a good handle on the specific changes
you have proposed. To make your work publishable, you would probably need to at
least publish the software and it appears
Hi, Huang.
It looks like you might need to add the rmarkdown package in Suggests (and
version bump to catch the change):
http://bioconductor.org/checkResults/devel/bioc-LATEST/ANCOMBC/nebbiolo2-buildsrc.html
Since the windows binary version is building, I'm guessing that may fix the
issue.
-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
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https://twitter.com/seandavis12
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t; >
> > Thanks,
> >Kevin
> >
> > [[alternative HTML version deleted]]
> >
> > __
> > R-package-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-package-devel
&g
> >> Bioc-devel@r-project.org mailing list
> >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >>
> >
> >
> > --
> >
> > Levi Waldron
> >
> > Associate Professor
> >
> > Department of Epidemiology and Biosta
without
> d3heatmap? Or is there an easy alternative to d3heatmap?
>
> Thanks,
> Mani
>
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Se
some larger packages from ‘Imports’ to
> ‘Suggests’, but to no avail.
>
> Best,
> Koen
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Be
On Tue, Mar 17, 2020 at 11:48 PM Julian Flesch
wrote:
> Hi Bioc team,
>
>
> I am the maintainer of the package /waddR/.
>
> We have had built issues on the active branch recently, due a dependency
> being unavailable. After pushing a patch, the issues were resolved on
> the devel branch.
>
> Is
There are some good ideas here that would provide enhancement to
BiocPkgTools. I don't have the bandwidth to incorporate right now, but
filing issues or a pull request with a skeleton would be helpful to keep
track.
Sean
On Sun, Feb 9, 2020 at 7:31 AM Vincent Carey
wrote:
> On Sat, Feb 8, 2020
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>
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ited. If you have
> received this message in error, please notify the sender immediately by
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ecipient to send a response
> to
> > the organizer and be added to the guest list, or invite others regardless
> > of their own invitation status, or to modify your RSVP. Learn more at
> > https://support.google.com/calendar/answer/37135#forwarding
> > ___
utational Genomics Group,
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> Phone: +393441130157
> E-mail: koustav@ifom.eu
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>
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On Tue, May 21, 2019 at 2:54 AM Aaron Lun <
infinite.monkeys.with.keyboa...@gmail.com> wrote:
> > Thanks for your response. So far my intention is to to plot them and I
> > do not intend on performing any other operation. The first step would be
> > read in the VCF file and transform it into a
s://bioconductor.org/packages/3.9/bioc/bin/macosx/el-capitan/contrib/3.6/GEOquery_2.51.5.tgz
'
Content type 'application/x-gzip' length 13828923 bytes (13.2 MB)
==
downloaded 13.2 MB
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Beth
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work.
Thanks,
Sean
(on behalf of the F1000Research Bioconductor Advisory Board)
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National Institutes of Health
Bethesda, MD 20892
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https://twitter.com/seandavis12
[[alternative HTML
I'd be interested to see one. I don't think it has been done yet.
On Fri, Feb 23, 2018 at 9:19 AM Michael Lawrence
wrote:
> Has anyone made a bioc interface to Hail yet? If not I might try to make
> one, just for fun.
>
> Michael
>
> [[alternative HTML version
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https://twit
This new NSF funding opportunity might interest a few folks on this list.
Sean
-- Forwarded message --
Subject: [SIAM-LS] New NSF funding opportunity: Rules of Life (RoL):
Forecasting and Emergence in Living Systems
Dear Colleagues:
NSF seeks to highlight the importance of
9] limma_3.34.2 xml2_1.1.1 readr_1.1.1 glue_1.2.0
> [13] purrr_0.2.4 hms_0.4.0compiler_3.4.2 pkgconfig_2.0.1
> [17] bindr_0.1tibble_1.3.4
>
>
> On Thu, Nov 30, 2017 at 11:56 AM, Leonardo Collado Torres
> <lcoll...@jhu.edu> wrote:
> >
3
> ------
> *From:* Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of Sean
> Davis <seand...@gmail.com>
> *Sent:* Friday, December 1, 2017 11:06:39 AM
> *To:* Michael Love
> *Cc:* bioc-devel@r-project.org
> *Subject:* Re: [Bioc-deve
The default user_cache_dir may not be the
best choice there.
Sean
>
> thanks,
> Mike
>
> ___
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Cent
On Thu, Nov 30, 2017 at 10:01 AM, Janssen-10, R.R.E. <
r.r.e.janssen...@umcutrecht.nl> wrote:
> Dear Martin,
>
> Martin writes:
>
> > On 11/29/2017 11:14 AM, Janssen-10, R.R.E. wrote:
> >> Hi Martin,
> >>
> >> Thanks for your reply!
> >>
> >> Martin Morgan writes:
> >>
> >>> On 11/29/2017 09:58
; On 30 November 2017 at 11:20, Sean Davis <seand...@gmail.com> wrote:
>
>> Thanks for the report, Mike.
>>
>> The problem was (specifically) in parsing a GSEMatrix file using a
>> filename. This should be fixed in versions 2.46.10 (release) and 2.47.12
>> (de
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> https://s
orresponding glyph status? :-P
>
I leave that as an exercise for the reader. ; )
Sean
>
> Thanks,
> H.
>
>
> On 11/17/2017 12:16 PM, Sean Davis wrote:
>
>> Just in case some developers would like to review the Bioconductor build
>> report as computabl
Just in case some developers would like to review the Bioconductor build
report as computable data in R:
http://bit.ly/2zKL3M3
Sean
--
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and/or confidential
> information. If you are not the intended recipient(s), or the employee or
> agent responsible for the delivery of this message to the intended
> recipient(s), you are hereby notified that any disclosure, copying,
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el.
>
> Thanks
> Nate
>
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r.org/packages/devel/bioc/html/oneSENSE.html
>
>
> --
> Best Wishes,
> Tan Yong Kee
>
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&
col is not
machine-type dependent, although how to use ssh keys may vary a bit,
particularly on windows.
Sean
>
> ~/.ssh$ ssh -T g...@git.bioconductor.org
> Permission denied (publickey).
>
> Thanks,
> Charles
>
>
>
> On Mon, Sep 4, 2017 at 5:28 PM, Sean Davis
; Washington, DC 20007
> Phone: (202) 687-1545
> Fax: (202) 687-5011
> http://icbi.georgetown.edu/boca
>
> [[alternative HTML version deleted]]
>
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(typo in the URL, missing or
mismatched ssh key) were overcome already. I'd proceed from there.
Hope that helps,
Sean
>
> Thanks,
> Charles
>
> On Mon, Sep 4, 2017 at 11:41 AM, Sean Davis <seand...@gmail.com> wrote:
>
>> Hi, Charles.
>>
>> The command
it/sync-
> > existing-repositories/
> > >
> > > However, if I run the command *git remote add upstream
> > > g...@git.bioconductor.org:packages/COHCAP.gi**t*, then I get an error
> > > message: *fatal: Not a git repository.*
> > >
> > >
&g
formation is strictly prohibited. If you have received this email
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> > Registergericht: Amtsgericht München HRB 6466
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>
>
> This email message may contain legally p
ats.
>
Again, mirrors are not included. I think the distinct IPs are reset per
month for the monthly stats.
>
> Regards,
>
> Lluís
>
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>
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tions?
>>
>> Thank you
>>
>> Greg Gloor
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Sorry I lead you astray, earlier, Maia.
In general, you do not need to install the package in the vignette. The
first code block in the vignette where you did "eval=FALSE" is the way to
go. The second code block where you actually do the installation is
unnecessary. The package is installed by R
ml). Perhaps I made an error
> somewhere?
>
> Best,
> Maia
>
> On Thu, Apr 20, 2017 at 1:24 PM, Sean Davis <seand...@gmail.com> wrote:
>
>> Hi, Maia.
>>
>> The git mirror is not used for building packages. Instead, you will need
>> to commit to svn f
Hi, Maia.
The git mirror is not used for building packages. Instead, you will need
to commit to svn for changes to show up on Bioconductor. See here for
details of working with git and svn together.
https://www.bioconductor.org/developers/how-to/git-mirrors/
If I misunderstood what you are
gt;
>>>
>>>
>>>
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>>>
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>>> https://stat.eth
Hi, Welliton.
Great question. Just out of curiosity, what are the internet connection
requirements that preclude running examples? Is authentication required?
Or are you connecting to a server that runs only intermittently?
Sean
On Tue, Mar 7, 2017 at 1:57 PM, Welliton Souza
Hi, all.
I am curious about what folks think about naming conventions for commonly
named functions, some of which are so common that even establishing a
generic would be difficult because of different use cases. Examples
include things like “filter”. One possibility is to use the Google Sheets
Github allows you to set the branch for the docs directory if I recall.
Perhaps a separate branch with a docs directory (not master) is a viable way to
go?
Sean
> On Dec 23, 2016, at 12:16 PM, Laurent Gatto wrote:
>
>
> There's actually another side-effect for
> On Nov 30, 2016, at 4:13 PM, Martin Morgan
> wrote:
>
> On 11/30/2016 08:51 AM, Kasper Daniel Hansen wrote:
>> Full transcript please; you're compiling from source.
>
> Excuse my ignorance about the Mac world but shouldn't these be available for
> binary
Thanks for the reply and feedback, Dirk.
> On Aug 23, 2016, at 10:59 AM, Dirk Eddelbuettel <e...@debian.org> wrote:
>
>
> hi Sean,
>
> On 23 August 2016 at 09:13, Sean Davis wrote:
> | I am trying to wrap a third-party toolkit that provides a C++ API. The
> co
I am trying to wrap a third-party toolkit that provides a C++ API. The code is
open source and includes a license that allows me to include it directly in an
R package. Right now, I am happy if I can get ANY build (linux, windows, or
Mac) working. The rough build process looks like that
Hi, Pabita.
This question is better asked on the bioconductor support site (
HTTPS://support.bioconductor.org). However, finding no evidence for
differential expression is not uncommon. Whether it is expected or not is
hard to comment on without data.
Sean
On Jul 30, 2016 10:43, "Pabita Basnet"
Hi, all.
Sorry for the hiccup. The problem appears to have stemmed from NCBI GEO
switching to using https for GEO data tables. This is not a highly-used
feature, but it was enough to break the build. It should be fixed (cross
fingers) in Devel. If fixed in devel, I will backport to
Forgive the really naive questions, but my C/C++ and Biostrings skills
are pretty rough. I have been playing with Rcpp to interface to an
external library for reading sequence formats. I am reading DNA
sequences one-at-a-time and would like to package a set of those up as a
DNAStringSet. I
/bioc_3_1_release/
.
That's a bit hands-on, as you sometimes have to go back several releases
to
see when it got removed, so hopefully Dan has a more reasonable approach.
Jim
On Thu, Aug 6, 2015 at 6:35 AM, Sean Davis seand...@gmail.com wrote:
Hi, Dan.
A user asked me a question about the DnaseR
Hi, Dan.
A user asked me a question about the DnaseR package. It appears to have
been removed from Bioc? Where would I find that out? What is the behavior
of the release/devel pages if a package has been previously removed?
Thanks,
Sean
[[alternative HTML version deleted]]
Hi, Vince.
It seems like knitr should be able to build a sweave vignette, particularly
if the stuff in the has been converted from sweave to knitr format?
It might be easier to do that than to convert the original to Rmarkdown.
Sean
On Mon, Aug 3, 2015 at 6:57 PM, Vincent Carey
Hi, Arne.
This question is best posted on the support site:
https://support.bioconductor.org/
To give a preview of the answer, though, while coverage and binned counts
are related concepts, they are not really identical. The csaw package is
looking for read counts.
Sean
On Tue, Jul 7, 2015
The last Bioconductor development cycle visualized as a graph using gource
is available here:
https://youtu.be/-HZ4XOh49fw
Sean
[[alternative HTML version deleted]]
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Bioc-devel@r-project.org mailing list
Hi, Aileen.
This list isn't really the best place to ask questions like this and is
really reserved for discussion around package development. Could you
please post to:
https://support.bioconductor.org/
That way, you benefit from more eyes and everyone benefits from potential
answers.
Thanks,
Hi, Wolfgang.
One way to think of docker is as a very efficient, self-contained virtual
machine. The operative term is self-contained. The docker containers
resemble real machines from the inside and the outside. These machines can
expose ports and can mount file systems, but something like
Is this a use case for a graphical build report that displays the build
status on a graph/DAG?
http://www.bioconductor.org/packages/release/bioc/vignettes/pkgDepTools/inst/doc/pkgDepTools.pdf
pkgDepTools, combined with a computable build report (a downloadable
version of the current build
the Views method has to handle that, and in my opinion return it
in
the order of cds list in this case. Anything else is way too fragile.
On Fri, Feb 20, 2015 at 8:14 AM, Sean Davis seand...@gmail.com wrote:
On Fri, Feb 20, 2015 at 8:10 AM, Malcolm Perry mgperr...@gmail.com
wrote:
Hi Sean
that works but is
nonsensical. I simply want to protect myself from making the same mistake
twice by some checking inside the Views() method.
Sean
Hope this helps,
Malcolm
On Fri, Feb 20, 2015 at 12:53 PM, Sean Davis seand...@gmail.com wrote:
I am calculating coverage metrics of a BAM
I am calculating coverage metrics of a BAM file on the CDS regions. When I
form the RangesList and do coverage(), the resulting coverage vector
applies the views to the regions from the RangesList without checking on
matching ordering or seqlevels of the RleList and the RangesList. This
results,
Hi, Martin, Val, and Herve.
This looks like a little problem with the bitnames in
Rsamtools/GenomicAlignments. Perhaps this is related to some bitnames
being deprecated?
Thanks,
Sean
library(GenomicAlignments)
sbp = ScanBamParam(which=cds[1:100],flag=scanBamFlag(isDuplicate = FALSE))
x =
On Sat, Nov 22, 2014 at 12:53 AM, Karl Stamm karl.st...@gmail.com wrote:
Question regarding gene name conversions. Once upon a time, I was doing a
lot of gene name conversions, particularly from NM_ to HGNC symbol or
Entrez GeneID. I used bioMaRt successfully, and developed a cache matrix
Hi, Darin.
You might find these instructions useful:
http://www.bioconductor.org/about/mirrors/mirror-how-to/
Basically, you can use rsync to get the repository and keep it up-to-date.
Sean
On Thu, Oct 30, 2014 at 9:17 AM, Darin Perusich da...@darins.net wrote:
Hello All,
Would it be
On behalf of a number of software developers, end-users, publishers
associated with the scientific analysis community, we would like to invite
all of you to review a document generated as a result of a NIH BD2K
supported meeting that focused on the opportunities and challenges of
developing a
Hi, Vince.
I'm coming a little late to the party, but I agree with Kasper's sentiment
that the less magical approach of using subsetByXXX might be the cleaner
way to go for the time being.
Sean
On Sat, Sep 20, 2014 at 10:42 AM, Vincent Carey st...@channing.harvard.edu
wrote:
Hi, Vince.
Looks like a good start. I'd probably pull all the assays from
ExpressionSet into SummarizedExperiment as the default, avoiding data
coercion methods that are unnecessarily lossy. Also, as it stands, the
assayname argument is not used anyway?
Sean
On Sat, Sep 20, 2014 at 10:38 AM,
with Sean, having tried implementing to magical alternative
--t
On Sep 20, 2014, at 9:31 AM, Sean Davis sdav...@mail.nih.gov
wrote:
Hi, Vince.
I'm coming a little late to the party, but I agree with Kasper's
sentiment
that the less magical approach of using
The National Institutes of Health is now accepting applications for
tenure-track positions through the Earl Stadtman recruitment mechanism.
Details are available here:
http://goo.gl/vF95Pi
Sean
[[alternative HTML version deleted]]
___
The National Institutes of Health is now accepting applications for
tenure-track positions through the Earl Stadtman recruitment mechanism.
Details are available here:
http://goo.gl/vF95Pi
Sean
[[alternative HTML version deleted]]
___
Hi, Arun. There is not such a system that covers the entire Bioconductor
project. Since packages are largely contributed by diverse developers,
there are many disparate bug tracking systems in use (and many packages
with no formal bug tracking). There is a facility in R to allow package
authors
Check in svn for the sources.
Sean
On Aug 8, 2014 8:58 AM, Kevin Rue-Albrecht kevin@ucdconnect.ie
wrote:
Hi,
Thank you for your replying.
Thanks Kasper, I had looked at other vignettes, but in the packages I
looked at so far I only found the PDF end-result. (e.g. edgeR), or the
On Fri, May 23, 2014 at 4:34 PM, Michael Lawrence
lawrence.mich...@gene.com wrote:
I like the idea about extracting important environmental information.
Possibly the function that browses to the bug tracker could print out the
sessionInfo for copy/paste.
It is tempting to push the automation
On Mon, Feb 24, 2014 at 2:22 AM, Hervé Pagès hpa...@fhcrc.org wrote:
Hi,
On 02/23/2014 03:58 AM, Sean Davis wrote:
On Sun, Feb 23, 2014 at 12:32 AM, Henrik Bengtsson h...@biostat.ucsf.edu
wrote:
Analogously to CRAN URL shortcuts, e.g.
http://cran.r-project.org/package=digest
On Sun, Feb 23, 2014 at 12:32 AM, Henrik Bengtsson h...@biostat.ucsf.eduwrote:
Analogously to CRAN URL shortcuts, e.g.
http://cran.r-project.org/package=digest
expanding to
http://cran.r-project.org/web/packages/digest/index.html,
it would be neat if Bioconductor would support
I doubt this is possible given the atomic nature of a git repository. You
might look at using a second git repository and including the minfi package
as a git submodule of that second repository. Then, you can keep things in
sync, but the minfi repository remains atomic.
Sean
On Feb 21, 2014
:
Hi Sean,
You can have a look at the 'bam2R' function from the 'deepSNV' package.
This will extract the base/insertion/deletion counts, base call
qualities,
and other metrics strand-specific from a BAM file.
Best wishes
Julian
On 13/02/14 17:09, Sean Davis wrote:
Hi
Hi, Martin.
How difficult would it be to include insertions/deletions in seq and qual
in the applyPileups method for PileupFiles? The use case is to look at the
context around variants for increases mismatch rates. Indels will have a
small impact on such calculations, but for completeness it
On Thu, Feb 13, 2014 at 1:12 PM, Martin Morgan mtmor...@fhcrc.org wrote:
On 02/13/2014 08:09 AM, Sean Davis wrote:
Hi, Martin.
How difficult would it be to include insertions/deletions in seq and qual
in the applyPileups method for PileupFiles? The use case is to look at
the
context
operation
would be useful.
Michael
On Wed, Feb 12, 2014 at 1:53 AM, Sean Davis sdav...@mail.nih.gov wrote:
It seems that the coverage method for BamFile() reads the entire BAM file
into memory and then calls coverage. Is there a coverage method for
BamFiles that does not read the entire
This isn't a direct answer to the question, but I recently learned of
this project:
http://www.dexy.it/
Basically, it is a giant set of filters that runs on text-based files
(MANY formats, including org) to produce outputs (MANY formats).
These filters include programming languages (including R)
A little off-topic, I know
NHGRI has released a new RFI. There are a number of folks on this
list that may have input they want to share, so I am forwarding along
the Notice:
http://grants.nih.gov/grants/guide/notice-files/NOT-HG-13-014.html
Sean
On Thu, Jul 11, 2013 at 11:01 AM, Kasper Daniel Hansen
kasperdanielhan...@gmail.com wrote:
On Thu, Jul 11, 2013 at 9:57 AM, Henrik Bengtsson
h...@biostat.ucsf.eduwrote:
On Wed, Jul 10, 2013 at 9:10 PM, Hervé Pagès hpa...@fhcrc.org wrote:
Hi Kasper,
On 07/10/2013 10:50 AM, Kasper
On Tue, Mar 26, 2013 at 7:27 AM, Ulrich Bodenhofer bodenho...@bioinf.jku.at
wrote:
On 03/26/2013 12:18 PM, Laurent Gatto wrote:
On 26 March 2013 09:26, Ulrich Bodenhofer bodenho...@bioinf.jku.at
wrote:
Dear colleagues,
One of my students is currently working on a package that we plan to
On Wed, Jan 23, 2013 at 1:41 PM, Frederic Fournier
frederic.bioi...@gmail.com wrote:
Hello everyone,
I recently submitted a package to bioconductor, and couple of days ago, the
package started to fail the automated daily build on george2 and moscato2.
Today I made some changes that work on my
Sorry for the simple question, but I am trying to read an unsigned
long long using the R readBin() function. Can someone point me in
the right direction, or am I better off using C for such things? The
file that I am reading will have been produced on the same machine
that is doing the reading.
On Jan 9, 2008 2:01 PM, Derek Stephen Elmerick [EMAIL PROTECTED] wrote:
Hello â
I am trying to write code that will read in multiple datasets;
however, I would like to skip any dataset where the read-in process
takes longer than some fixed cutoff. A generic version of the function
is the
On Jan 1, 2008 12:36 PM, Uwe Ligges [EMAIL PROTECTED]
wrote:
Thank you, Henrik! This saves us a lot of time!
Uwe
Henrik Bengtsson wrote:
On 01/01/2008, Henrik Bengtsson [EMAIL PROTECTED] wrote:
Also make sure the problem is not due to downloading a gzip file in
text mode, because to
I have been trying to use the gunzip function in the R.utils package. It
opens a connection to a gzfile, uses readBin to read from that connection,
and then uses writeBin to write out the raw data to a new file. This works
as expected under linux/mac, but under Windows, I get:
Error in
working directory.
The actual gunzip function is pretty bare bones, so I don't think it
complicates matters much to use it in this example.
Sean
On Dec 31, 2007 1:24 PM, Uwe Ligges [EMAIL PROTECTED]
wrote:
Can you give a reproducible example, pelase?
Uwe Ligges
Sean Davis wrote:
I have
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