On Thu, Jun 4, 2015 at 1:50 PM, James W. MacDonald jmac...@uw.edu wrote:
In the last release, the warning message from select() telling people that
their results include one-to-many mappings was removed. While some may find
this warning annoying, I think silently returning something unexpected
don't use set.seed inside a package; that control
should
completely be left to the user.
Best,
Kasper
On Wed, Jun 3, 2015 at 7:08 AM, Vincent Carey
st...@channing.harvard.edu
wrote:
This document indicates how to achieve reproducibility independent
assigning the proper seqinfo for relationships
is very fast.
That's all I was getting at...
Statistics is the grammar of science.
Karl Pearson http://en.wikipedia.org/wiki/The_Grammar_of_Science
On Wed, Jun 3, 2015 at 12:17 PM, Vincent Carey st...@channing.harvard.edu
wrote:
I typically
I typically get this info from Homo.sapiens. The result is parasitic on
the TxDb that is in there. I don't know how easy it is to swap alternate
TxDb in to get a different build. I think it would make sense to regard
the OrganismDb instances as foundational for this sort of structural data.
On
On Wed, Jun 3, 2015 at 5:17 PM, Vincent Carey st...@channing.harvard.edu
wrote:
Hi, this question belongs on R-help, but perhaps
https://stat.ethz.ch/R-manual/R-devel/library/parallel/html/RngStream.html
will be useful.
Best regards
On Wed, Jun 3, 2015 at 3:11 AM, Yu, Guangchuang g
Hi, this question belongs on R-help, but perhaps
https://stat.ethz.ch/R-manual/R-devel/library/parallel/html/RngStream.html
will be useful.
Best regards
On Wed, Jun 3, 2015 at 3:11 AM, Yu, Guangchuang g...@connect.hku.hk wrote:
Dear all,
I have an issue of setting seed value when using
Agreed that the workflow vehicle should get more attention. Do all
workflows correspond to packages?
On Tue, May 12, 2015 at 7:31 PM, Michael Lawrence lawrence.mich...@gene.com
wrote:
I like the idea of having multiple, domain-specific cores. Those could also
serve as a vehicle for
Please provide sessionInfo()
The class is defined in AnnotationHub in devel. Perhaps it is not suitably
exported.
On Thu, Apr 9, 2015 at 5:33 AM, Ludwig Geistlinger
ludwig.geistlin...@bio.ifi.lmu.de wrote:
Hi,
As I pulled down the devel_core image (running boot2docker under OS X
Yosemite)
On Mon, Mar 30, 2015 at 2:10 PM, Katie Planey katie.pla...@gmail.com
wrote:
Hi all,
I'm packaging my code for a meta-clustering method to submit to
Bioconductor, and I have the following design dilemma: my method can be
used on either a matrix of gene expression data (well really any
Clearly I should have checked the release calendar more carefully before
commenting.
I lost track of the transition of R versions.
On Sun, Mar 22, 2015 at 2:57 PM, Dan Tenenbaum dtene...@fredhutch.org
wrote:
- Original Message -
From: Vincent Carey st...@channing.harvard.edu
FWIW I encountered a similar situation a couple of weeks ago. I should
have said something, I guess.
On Tue, Mar 10, 2015 at 2:08 PM, Kasper Daniel Hansen
kasperdanielhan...@gmail.com wrote:
Ok, I had to manually remove the BiocInstaller package, restart R and then
run biocLite and I am now
On Wed, Mar 4, 2015 at 12:01 PM, Robert Castelo robert.cast...@upf.edu
wrote:
some of the goals behind this discussion are IMO similar to the ones for
biocMultiAssay:
https://github.com/vjcitn/biocMultiAssay
maybe Vince can confirm.
It is true that there are connections between the
On Wed, Mar 4, 2015 at 5:21 PM, Kevin Coombes kevin.r.coom...@gmail.com
wrote:
HI,
I'm following this discussion with interest, for the following reason.
There are more than a dozen packages that I have written and still
maintain. Most of them were started while I was at M.D. Anderson ,
I am a bit concerned about any major alterations to the
SummarizedExperiment API. We have
two papers and plenty of working code that use it in meaningful ways.
Effort required to keep new
formulations back-compatible as well as bug-free has to be weighed
seriously.
I agree that the name is not
Gviz has a nice way of working with TxDb instances to derive gene models.
It can be cumbersome to refer to a TxDb instance, and the Homo.sapiens
OrganismDb instance is very convenient to work with.
I do not see any straightforward way to extract a reference to a TxDb from
Homo.sapiens. I could
Clearly I dropped the ball on this. Is the iterative approach to
discovering and
specifying the additional headers, given by Steffen Neumann on 5/2/13,
still valid?
I would like to use BH if possible for maintaining RBGL. However I won't
be able
to get involved until March at the earliest.
On
Yes, based on the query to the list, it seemed to me someone was having
trouble
finding out what can be/needs to be specified. There are a lot of options
and the little widget
you've sketched is going to be useful.
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On Mon, Dec 8, 2014 at 11:22 AM, Sonali Arora sar...@fredhutch.org wrote:
Hi Vince,
On 12/8/2014 7:38 AM, Vincent Carey wrote:
Very nice. Is WholeGenomeData under SequencingData sufficiently
clear?
We mirrored the Technology category under Software biocViews for
TechnologyData, thus
http://exac.broadinstitute.org/
there are 2.9 GB of vcf at
ftp://ftp.broadinstitute.org/pub/ExAC_release/release0.2/
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fwiw sos::findFn(narrow) produces quite a few hits, including
http://finzi.psych.upenn.edu/R/library/GenomicRanges/html/intra-range-methods.html
it may be more effective to parse doc than to hope that the formal metadata
will yield the desired fruit?
On Thu, Dec 4, 2014 at 1:26 PM, Martin
On Thu, Nov 20, 2014 at 12:17 PM, Thomas Girke thomas.gi...@ucr.edu wrote:
Hi Valerie,
Excellent. In addition to collecting log outputs, I have a few more
suggestions that may be worth considering:
- Collecting the results form parallel computing tasks directly in an R
object is a great
On Mon, Nov 10, 2014 at 12:19 PM, Martin Morgan mtmor...@fredhutch.org
wrote:
On 11/09/2014 11:06 AM, Dan Tenenbaum wrote:
- Original Message -
From: Martin Morgan mtmor...@fredhutch.org
To: Laurent Gautier lgaut...@gmail.com, bioc-devel@r-project.org
Sent: Sunday, November 9,
This is potentially a good question but it is not very clear and it is not
a devel-level
question. Post the question to support.bioconductor.org after reading the
posting guide
and I'd bet you get lots of useful advice from people with similar
situations. In fact
if that does not work, because
On Tue, Oct 28, 2014 at 2:29 PM, Hervé Pagès hpa...@fredhutch.org wrote:
Hi,
On 10/28/2014 08:48 AM, Vincent Carey wrote:
On Tue, Oct 28, 2014 at 11:23 AM, Kasper Daniel Hansen
kasperdanielhan...@gmail.com wrote:
Well, first I want to make sure that there is not something special
There is a README.txt in the pkgs folder.
I will attach it. I think this is accurate, but there may be something
else on the site.
On Thu, Oct 23, 2014 at 10:23 PM, Henrik Bengtsson h...@biostat.ucsf.edu
wrote:
It's been a while since I worked with experimental packages. Where
can I find
.
~G
On Sat, Sep 20, 2014 at 11:38 AM, Vincent Carey
st...@channing.harvard.edu
wrote:
OK by me to leave [ alone. We could start with subsetByEntrez,
subsetByKEGG, subsetBySymbol, subsetByGOTERM, subsetByGOID.
Utilities to generate GRanges for queries in each of these vocabularies
mtmor...@fhcrc.org
wrote:
On 10/11/2014 08:41 AM, Vincent Carey wrote:
Is there anything on the order of as([GeneSet], GRanges) around?
no, I don't think so; obviously of use and following a common theme.
Martin
On Sat, Sep 20, 2014 at 11:34 PM, Gabe Becker becker.g...@gene.com
wrote
On Mon, Sep 22, 2014 at 10:17 AM, Cook, Malcolm m...@stowers.org wrote:
Hi,
https://github.com/vjcitn/biocMultiAssay/blob/master/vignettes/SEresolver.Rnw
shows some modifications to [ that allow subsetting of SE by
gene or pathway name
Without reading the code, do you intend that
On Sat, Sep 20, 2014 at 11:38 AM, Vincent Carey
st...@channing.harvard.edu
wrote:
OK by me to leave [ alone. We could start with subsetByEntrez,
subsetByKEGG, subsetBySymbol, subsetByGOTERM, subsetByGOID.
Utilities to generate GRanges for queries in each of these vocabularies
should
this is coming out of the build system for GGtools ... not easy to find as
the
problem seems to cause emission of megabytes of warnings
illuminaHumanv1CHR is deprecated as the data is better accessed from
another location. Please use an appropriate TxDb object or package for
this kind of
On Sun, Sep 21, 2014 at 11:07 AM, Martin Morgan mtmor...@fhcrc.org wrote:
On 09/21/2014 07:44 AM, Vincent Carey wrote:
this is coming out of the build system for GGtools ... not easy to find as
the
problem seems to cause emission of megabytes of warnings
illuminaHumanv1CHR is deprecated
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:
https://github.com/vjcitn/biocMultiAssay/blob/master
character, so should just work
most of the time, but as I said it's early days; lots more testing for
functionality and usefulness is needed.
~G
On Sat, Sep 20, 2014 at 11:38 AM, Vincent Carey
st...@channing.harvard.edu wrote:
OK by me to leave [ alone. We could start with subsetByEntrez
For GRanges x, my naive expectation is that genome(x) returns a length-
one tag identifying the genome to which chromosomal coordinates
correspond. The genome() method seems to have sequence-specific
semantics, which makes sense, but when we identify sequence
with chromosome, it seems too
to share since IIRC he requested the addition of the
genome field a couple of years ago and made the case for having it
defined at the sequence level.
Cheers,
H.
On 09/08/2014 07:21 AM, Vincent Carey wrote:
For GRanges x, my naive expectation is that genome(x) returns a length-
one tag
good use cases to share since IIRC he requested the addition
of the
genome field a couple of years ago and made the case for having
it
defined at the sequence level.
Cheers,
H.
On 09/08/2014 07:21 AM, Vincent Carey wrote
On Fri, Sep 5, 2014 at 7:50 PM, Peter Haverty haverty.pe...@gene.com
wrote:
Hi all,
I respectfully disagree. One should certainly check in each discrete unit
of work. These will often not result in something that is ready to be used
by someone else. Bumping the version number constitutes
here's the guide i am aware of. a link should be on the basic workflow
page as a 'how to'.
https://hedgehog.fhcrc.org/bioconductor/trunk/madman/workflows/README.md
On Wed, Sep 3, 2014 at 7:47 AM, Michael Love michaelisaiahl...@gmail.com
wrote:
hi,
I'd like to contribute a workflow, but I
I just noticed that the addresses for NHGRI GWAS catalog distribution
are relative to GRCh38. Is there a plan for using Homo.sapiens with
selection of build? It may not be uncommon for someone to want to
work with different builds.
What would be useful for me at this time is a simple way to get
good marking of which build
is in use on all our ranges, IMHO.
On Mon, Jul 28, 2014 at 1:14 PM, Vincent Carey st...@channing.harvard.edu
wrote:
I just noticed that the addresses for NHGRI GWAS catalog distribution
are relative to GRCh38. Is there a plan for using Homo.sapiens with
selection
On Tue, Jul 22, 2014 at 7:10 PM, Andrzej OleÅ andrzej.o...@gmail.com
wrote:
Hi Dan, Michael, Julian,
Thank's for keeping the links to the tarballs!
I don't argue that mixing release and devel is a good idea in general.
Rather, that for some users this might be the best compromise between
On Thu, Jul 10, 2014 at 7:05 PM, Michael Lawrence lawrence.mich...@gene.com
wrote:
On Thu, Jul 10, 2014 at 2:16 PM, Steve Lianoglou lianoglou.st...@gene.com
wrote:
Hi,
On Thu, Jul 10, 2014 at 1:52 PM, Vincent Carey
st...@channing.harvard.edu wrote:
a new, more inclusive GWAS catalog
Sounds nice but we have to be careful. We may need a parameter:
Homo.sapiens(hg19) ... because
broad adoption of new builds may take considerable time.
On Wed, Jun 18, 2014 at 6:13 PM, Hervé Pagès hpa...@fhcrc.org wrote:
On 06/18/2014 05:26 AM, Michael Lawrence wrote:
Would it make sense
2).
Martin
Martin
On Thu, Apr 24, 2014 at 1:44 PM, Vincent Carey
st...@channing.harvard.eduwrote:
+1. this will be a good motivation for maintainers to get the CITATION
entry right.
On Thu, Apr 24, 2014 at 3:39 PM, Wolfgang Huber whu...@embl.de wrote:
I wonder whether
Lawrence lawrence.mich...@gene.com
wrote:
I was just about to say that this should be a nice carrot for authors to
start improving their citations...
On Fri, May 30, 2014 at 6:27 AM, Vincent Carey st...@channing.harvard.edu
wrote:
Very nice. We'll give it a couple of weeks and then announce
urls, browsers ... :(
how about a variation on utils:: bug.report in biobase? each package could
have a bugReportHandle method that is called when reportBug is called with
the package name as argument. the biobase version would gather key
environmental information at the time of the call and
i think they should probably move, but i wonder if S4Vectors is the right
destination.
is the row concept vector-like? i was looking for rowQ recently and
expected it to be in genefilter...
On Fri, May 16, 2014 at 11:04 AM, Michael Lawrence
lawrence.mich...@gene.com wrote:
Would it make
as far as i know it is indeed possible and you just use the AMI EC2
management interface to do it. the details are not at hand ... you could
look at the AMI identified in the eQTL workflow and i think it does have a
larger disk than 40 but how i got there i cannot recall
On Fri, May 9, 2014 at
+1. this will be a good motivation for maintainers to get the CITATION
entry right.
On Thu, Apr 24, 2014 at 3:39 PM, Wolfgang Huber whu...@embl.de wrote:
I wonder whether the software that makes the package landing pages (e.g.:
http://bioconductor.org/packages/release/bioc/html/minfi.html )
seems like something we should use more routinely, and it was not
straightforward for me to find it in IRanges
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i can't confirm this
library(GenomicRanges)
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport,
On Wed, Mar 19, 2014 at 4:00 PM, Michael Lawrence lawrence.mich...@gene.com
wrote:
It would be nice to have functions like isSNV, isIndel, isDeletion, etc
that at least provide precise definitions of the terminology. I've added
these, but they're designed only for VRanges. Should work for
c(x[[1]][1:3,1:2], x[[3]][1:3,1:2]) # this works
GRanges with 6 ranges and 2 metadata columns:
seqnames ranges strand |paramRangeIDREF
RleIRanges Rle |factor DNAStringSet
[1]1 [ 10583, 10583] * | dhs_chr1_10402
Streamer package has DAGTeam/DAGParam components that I believe are
relevant.
An abstraction of the reduction plan for a parallelized task would seem to
have a natural
home in BatchJobs.
On Thu, Nov 14, 2013 at 8:15 AM, Michael Lawrence lawrence.mich...@gene.com
wrote:
Hi guys,
We often
Thanks Tim
We are collecting relevant resources in
https://github.com/vjcitn/biocMultiAssay
I will add your class definition as TTMergedDataSet
we have some TCGA data (affy expression, RNA seq, miRNA) in inst/extdata
from Levi Waldron. Currently
these are all ExpressionSet instances. I will
I am falling behind. I wanted to have a prototype of the following but I
won't do it for a while.
We need to make it more convenient to get the right seqinfo metadata in
place for a wide variety of artifacts.
i propose that there has to be a softer landing for unmet expectations, and
some
for some approaches to working with large matrices in R, please look at
http://cran.r-project.org/web/views/HighPerformanceComputing.html
scroll down to Large memory and out-of-memory data
i suspect this view text should be enlarged to include rhdf5 and ncdf
as additional
relevant resources
On
should approaches to fault-tolerance/recovery/debugging be a topic here?
On Thu, Nov 15, 2012 at 1:53 PM, Henrik Bengtsson h...@biostat.ucsf.eduwrote:
Is there any write up/discussion/plans on the various types of
parallel computations out there:
(1) one machine / multi-core/multi-threaded
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