Hi Weijun,
I restored the old URLs for all packages but instead of
showing the new stats, the page at the old URL says the stats
has moved and the new URL is provided. See for example:
http://bioconductor.org/packages/stats/bioc/pathview.html
Cheers,
H.
On 05/12/2016 10:57 PM, Hervé Pagès
rtive
evidence claimed does not even exist. Not sure how that may affect our grant
application.
can we still keep the old URL or at least make it a alias to the new one? Thank
you!
Weijun
On Thu, 5/12/16, Hervé Pagès wrote:
Subject: [Bioc-deve
eedback welcome.
Cheers,
H.
PS: Updated stats for annotation and experiment packages coming soon.
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpa..
packages and years in it.
Best wishes
Wolfgang
On May 5, 2016, at 21:03 GMT+2, Hervé Pagès wrote:
Hi,
The download report is actually about to change. See:
https://bioconductor.org/packages/new-stats/bioc/Biobase/
for how the new stats are going to look. This is work in progress
[[alternative HTML version deleted]]
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailm
__
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 981
,
with.utr3_len=with.utr3_len, filter=filter))
})
cheers, jo
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
Hervé Pagès
Program in Computational Biology
Division of Public
fined on my package.
This
stems from a finalizer on a class defined in a package imported by my
package (GenomeInfoDb), which I'm guessing is detached from the
environment
before this finalize function is called.
Any ideas on how to avoid this error?
Package source here:
https://github.com/b
ethz.ch/mailman/listinfo/bioc-devel
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpa...@fredhutch.org
Phone: (2
On 04/27/2016 04:24 AM, Michael Lawrence wrote:
On Tue, Apr 26, 2016 at 11:12 PM, Hervé Pagès wrote:
Hi,
I would not discard defining a SummarizedExperiment subclass so quickly.
SummarizedExperiment is very generic and can contain any kind of data.
IIUC the csaw package uses
On 04/27/2016 03:18 AM, Martin Morgan wrote:
On 04/27/2016 02:12 AM, Hervé Pagès wrote:
Hi,
I would not discard defining a SummarizedExperiment subclass so quickly.
SummarizedExperiment is very generic and can contain any kind of data.
IIUC the csaw package uses SummarizedExperiment to
ified that any disclosure,
copying, distribution, or use of this email message is prohibited. If
you have received this message in error, please notify the sender
immediately by e-mail and delete this email message from your
computer. Thank you.
___
Bi
8WHE_O0PrI0B
-0yS
t37UGJMdDhnwk0JFoVzS5Cw&s=3ZMFBJ4XMwlGXkfXcB5spcBnnzqBDeqk05sf_TSi88g
&e=
___
Bioc-devel@r-project.org mailing list
https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailm
an_listinfo_bioc-2Ddevel&d=BQIFaQ&c=WJBj9sUF1
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024
E-mail
de in an environment (inheriting from the base namespace) where
import(), export(), etc, were defined. Maybe there's a good reason why
it was not implemented that way.
I'm sure there is ;-)
H.
On Fri, Apr 1, 2016 at 12:55 PM, Hervé Pagès wrote:
On 03/31/2016 04:07 PM, Michael Lawrenc
(But is has been a while since I've worked on this code).
Best,
luke
On Thu, 31 Mar 2016, Karim Mezhoud wrote:
I think "From" is needed to specify which package we want to exlude
functions.
I think excludeFrom (package, function) seems to be intuitive.
thanks,
Karim
On T
is a very interesting idea and works for me! Thanks!
importPatternFrom(IRanges, "^values$")
Best,
Julie
On 3/31/16 2:51 PM, "Bioc-devel on behalf of Hervé Pagès"
wrote:
On 03/30/2016 08:35 PM, Michael Lawrence wrote:
That would work, but R is not going to be happy about re
an/listinfo/bioc-devel
[[alternative HTML version deleted]]
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-
__
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 9810
University of Sydney
Camperdown NSW 2050
Australia
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave
e function. I'm curious what other developers think would be
best practice for where/how to store this message content in a
package.
best,
Mike
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
Hervé Pa
0.1 RUnit_0.4.31 KernSmooth_2.23-15 stringi_1.0-1
[37] RCurl_1.95-4.8
biocLite("BiocUpgrade")
Error: Bioconductor version 3.2 cannot be upgraded with R version 3.2.3
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinf
e
[[alternative HTML version deleted]]
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N,
Cheers,
Pete
On Thu, 3 Mar 2016 at 13:31 Hervé Pagès wrote:
Hi Pete,
On 03/02/2016 12:42 PM, Peter Hickey wrote:
This is mostly directed to Herve and/or Martin, but I'd be interested
in other's input too.
The SummarizedExperiment package defines rbind,Assays-method and
cbind,Assa
ersen
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-10
would be cleaner,
the contracts simpler, and the methods easier to implement. Also
we wouldn't need to depend on the abind package.
What do you think?
H.
Cheers,
Pete
_______
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/lis
ject.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Re
lt;-, rbind,
and cbind but these capabilities are not needed by popular workflows
like the DESeq2 vignette.
That being said, I don't know the reason for the current 4 dimensions
limit of subsetting. Sounds kind of arbitrary. Maybe we should just
support subsetting of assays with any number
you earlier though.
H.
Dario Strbenac
PhD Student
University of Sydney
Camperdown NSW 2050
Australia
devteam-bioc mailing list
To unsubscribe from this mailing list send a blank email to
devteam-bioc-le...@lists.fhcrc.org
o Strbenac
PhD Student
University of Sydney
Camperdown NSW 2050
Australia
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fa
lia
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O.
specify *absolute* positions, I don't think that
works. How would you call restrict() with these arguments to perform
Dario's strand-specific trimming?
H.
Kasper
On Tue, Feb 16, 2016 at 3:41 AM, Hervé Pagès mailto:hpa...@fredhutch.org>> wrote:
Hi Dario,
AFAIK the '
-
Dario Strbenac
PhD Student
University of Sydney
Camperdown NSW 2050
Australia
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutch
sibly
things other than subsetting break as well in this case).
# No error
y <- makeSE(5)
y
# Error
y[1, ]
Perhaps there should be a check in the constructor that all assay
elements have < 5 dimensions?
Cheers,
Pete
___
Bioc-devel@r-project.org ma
les found for 'unlist'
Is this a problem with moscato2? I don’t get this if I build locally…
best
Thomas
[[alternative HTML version deleted]]
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
chael Love
Sent: Monday, February 1, 2016 3:35 PM
To: Dan Tenenbaum
Cc: bioc-devel; Hervé Pagès
Subject: Re: [Bioc-devel] TIMEOUTs on Morelia
I was able to construct a minimal example where it seems the bug originates
from SummarizedExperiment:
library(SummarizedExperiment)
se <- SummarizedEx
#x27;x' and 'i' is
enough and allows the assay() setter to take any matrix-like object as
long as the resulting SummarizedExperiment object is valid.
These 2 changes are in SummarizedExperiment 1.1.17.
Thanks for the suggestions,
H.
Cheers,
Pete
______
"Ensembl"
note that now if you have a UCSC-style GRanges object like this one:
gr <- GRanges(c("chr1", "chr2"), IRanges(c(10, 20), c(30, 40)))
seqlevelsStyle(gr)
[1] "UCSC"
that you want to use with the BSgenome object, the following simple
operati
ately by e-mail and delete this email message from your
computer. Thank you.
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Scien
n which I’m not aware of.
Thanks for help or any alternative solutions!
jo
_______
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
F
On 01/13/2016 07:28 PM, Hervé Pagès wrote:
Hi Ben, Martin,
On 01/13/2016 08:19 AM, Morgan, Martin wrote:
[...]
So this is a bug in S4Vectors, but fixed in Bioc-devel where new
package development should be occurring.
I'll leave it to Herve or others to decide whether S4Vectors in
re
version deleted]]
This email message may contain legally privileged 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, cop
ns.UCSC.knownGene to have an easy starting point for the
analysis of human data.
cheers,
robert.
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
[[alternative HTML version deleted]]
__
016-01-11 14:10:24 -0800 (Mon, 11 Jan 2016)
# GenomicFeatures version at creation time: 1.23.16
# RSQLite version at creation time: 1.0.0
# DBSCHEMAVERSION: 1.1
Note the new "UCSC Track" field above.
Cheers,
H.
On 01/11/2016 01:12 PM, Hervé Pagès wrote:
Hi Robert and others,
I looked
ations anchored at Entrez IDs, at least what
is called the "basic set", similarly to what is done with
TxDb.Hsapiens.UCSC.knownGene to have an easy starting point for the
analysis of human data.
cheers,
robert.
___
Bioc-de
itFile.
Martin
From: Bioc-devel [bioc-devel-boun...@r-project.org] on behalf of Rainer
Johannes [johannes.rai...@eurac.edu]
Sent: Saturday, January 09, 2016 11:01 AM
To: Hervé Pagès
Cc: Michael Lawrence; Martin Morgan
Subject: Re: [Bioc-devel] Problem with seq
ls<-,TwoBitFile for that particular
use case. Just wanted to mention that the ability to rename the
sequences in a TwoBitFile, FastaFile, or other file-based object that
supports seqinfo() would be useful in general.
H.
On Fri, Jan 8, 2016 at 11:04 AM, Hervé Pagès wrote:
Hi Jo, Mi
man/listinfo/bioc-devel
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
He
s or code examples?
Thanks,
Sean
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/b
This is fixed in S4Vectors release (0.8.6) and devel (0.9.16).
Cheers,
H.
On 01/04/2016 11:52 AM, Hervé Pagès wrote:
Hi Malcolm,
Thanks for reporting this. Will fix.
H.
On 01/04/2016 10:53 AM, Malcolm Perry wrote:
Hello,
A recent question on the support site (
https
library(GenomicRanges)
gr = GRanges("chr", IRanges(1, 5))
mcols(gr) = data.frame(name="range1")
[[alternative HTML version deleted]]
_______
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-
call to `as(x, "numeric")` dispatches the coerce
S4 method for the signature `c("integer", "numeric")`, whose body is
copied in below.
function (from, to = "numeric", strict = TRUE)
if (strict) {
class(from) <- "numeric"
from
-
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-
how to map GRCh38 seqlevels to
hg38 seqlevels.
H.
Michael
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchins
On 12/15/2015 03:13 PM, Michael Lawrence wrote:
On Tue, Dec 15, 2015 at 2:15 PM, Hervé Pagès wrote:
SummarizedExperiment has long been supporting unidimensional subsetting
which was subsetting by row. However the length of any SE object was
always considered to be 1 which was confusing. The
-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024
E-mail
0; Fax: 202-687-5011
http://icbi.georgetown.edu/
-------
On Fri, Dec 11, 2015 at 3:38 PM, Hervé Pagès mailto:hpa...@fredhutch.org>> wrote:
Hi Krithika,
NSBS() is the internal helper defined in the S4Vectors package that
takes care of
5-10-14 Bioconductor
yaml2.1.13 2014-06-12 CRAN (R 3.2.0)
zlibbioc1.16.0 2015-10-14 Bioconductor
Thanks,
--Krithika
[[alternative HTML version deleted]]
___
Bioc-devel@r-project.org
start = 1L, width = n)
7: .local(x, ...)
8: head(x, 3)
9: head(x, 3)
Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
Selection:
___
Bioc-devel@r-project.org
EMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats4parallel stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] GenomicRanges_1.22.1 GenomeInfoDb_1.6.1 IRanges_2.4.4
[4] S4Vectors_0.8.3 BiocGenerics_0.16.1
loaded via a namespace (and n
think).
Cheers,
H.
[[alternative HTML version deleted]]
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Cent
d
delete this email message from your computer. Thank you.
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N,
yourself to support those then it may be worth the
effort?
We're adding this to our backlog. Will take a couple of weeks before
we get this done.
Cheers,
H.
Thomas
On Tue, Dec 1, 2015 at 1:17 PM Hervé Pagès mailto:hpa...@fredhutch.org>> wrote:
Hi Malcolm,
On 12/01/2015 12:
Hi Malcolm,
On 12/01/2015 12:29 PM, Cook, Malcolm wrote:
-Original Message-
> From: Bioc-devel [mailto:bioc-devel-boun...@r-project.org] On Behalf Of
> Hervé Pagès
> Sent: Monday, October 26, 2015 12:39 PM
> To: Thomas Girke ; Arora, Sonali
> ; bioc-deve
Tools.
thanks,
Stephanie
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Bo
think that a significant proportion
of naive end users would get tripped up by that if the warning weren't
there. They still might be, but at least we gave them a chance.
Anyway, it took like three lines of code to make it work consistently
for many:many mappings, so that's what I did.
B
On 11/20/2015 03:21 PM, Hervé Pagès wrote:
Hi Jim,
I think we should choose the biomaRt model, that is, duplicated are
allowed but silently ignored.
Note that this is also the SQL model. When you do
SELECT * FROM ... WHERE key IN c('key1&#x
es be removed
before querying the database, preferably with a message saying that dups
were removed?
2. If the answer to #1 is yes, then to be consistent, I will just commit
the patch I have made to both devel and release.
Best,
Jim
--
Hervé Pagès
Program in Computation
Developers,
On 11/16/2015 11:39 PM, Hervé Pagès wrote:
Hi Aaron,
On 11/16/2015 09:39 AM, Hervé Pagès wrote:
[...]
Anyway, you convinced me that we should not try to follow too closely
the names model for how we treat metadata columns. If nobody objects,
I'll change the behavior o
Gabriel Becker, Ph.D
Associate Scientist
Bioinformatics and Computational Biology
Genentech Research
[[alternative HTML version deleted]]
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
Hervé Pag
Hi Aaron,
On 11/16/2015 09:39 AM, Hervé Pagès wrote:
Hi Aaron,
On 11/15/2015 12:37 PM, Aaron Lun wrote:
Hi Herve,
I would have expected GRanges behaviour, where the metadata is affected
by the replacement. For example, with GRanges objects, I often use the
metadata to store statistics or
HTML version deleted]]
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave.
objects,
I'll change the behavior of the various "replaceROWS" methods in the
S4Vectors stack and make sure that they all transfer the metadata
columns from 'value' to 'x'.
Cheers,
H.
Cheers,
Aaron
Hervé Pagès wrote:
Hi Aaron,
On 11/15/2015 10:59 AM, Aaron
LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats4stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] SummarizedExperiment_1.1.2 Biobase_2.31.0
[3] GenomicRanges_1.23.3
https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpa...@fredhutch.org
Phone: (206) 667-57
all takes the remaining 1/2 of the
time. I was thinking it might be possible to make this quite fast by
looping over the GRanges object at the C-level and breaking out of the
loop if gr[i+1] <= gr[i] or gr[i+1] < gr[i], as appropriate. Does this
sound reasonable?
Cheers,
Pete
On 3 November
__
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
[[alternative HTML version deleted]]
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
Hervé Pagès
Program
Matrix_1.2-2 checkmate_1.6.2
[13] proto_0.3-10 GOstats_2.37.0 splines_3.3.0
[16] stringr_1.0.0 pheatmap_1.0.7 RCurl_1.95-4.7
[19] biomaRt_2.27.0 munsell_0.4.2 sendmailR_1.2-1
[22] rtracklayer_1.31.1 base64enc_0.1-3 BBmisc_1.9
[25] fail_1.3 edgeR_3.13.0 XML_3.98-1.3
[28] AnnotationForge_1.13.0 MASS_7.3-44 bit
ot;[<-" method for Vector objects (defined
in S4Vectors) does (thru the default method for
normalizeSingleBracketReplacementValue).
Thanks,
H.
Michael
On Wed, Oct 21, 2015 at 11:14 AM, Hervé Pagès mailto:hpa...@fredhutch.org>> wrote:
Hi Michael,
On 10/21/2015 07:09 AM, Michael
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
[[alternative HTML version deleted]]
_______
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
Hervé Pagès
Progr
3. None of the reasons you listed as causing an implicit attach seems to
apply here.
Thanks,
Marcin
On Mon, Oct 19, 2015 at 5:56 PM, Hervé Pagès mailto:hpa...@fredhutch.org>> wrote:
Hi Marcin,
On 10/19/2015 05:11 AM, Marcin Cieślik wrote:
Dear Bioc Developers,
masked from ‘package:parallel’:
[[alternative HTML version deleted]]
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Scien
airs in readGAlignmentPairs, but not in
GAlignmentPairs itself; could be mistaken though...
Martin
From: Michael Lawrence [lawrence.mich...@gene.com
<mailto:lawrence.mich...@gene.com>]
Sent: Saturday, October 17, 2015 9:48 AM
bioc-devel
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1
On 10/16/2015 10:52 AM, Dan Tenenbaum wrote:
- Original Message -
From: "Hervé Pagès"
To: "Dan Tenenbaum" , "Levi Waldron"
Cc: "bioc-devel"
Sent: Friday, October 16, 2015 10:07:03 AM
Subject: Re: [Bioc-devel] BioC 3.2 branch created
Hi Da
org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Res
exact
strand of the location is unknown, or irrelevant, or when the "feature"
at that location belongs to both strands. A pair with discordant strand
belongs to both strands. Also there is a lot of code around that
assumes strand() never returns NAs.
H.
On Fri, Oct 16, 2015 at 9:15
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024
clearly a misnomer and a source of confusion.
H.
On Wed, Sep 30, 2015 at 9:37 PM, Hervé Pagès mailto:hpa...@fredhutch.org>> wrote:
On 09/30/2015 05:28 PM, Michael Lawrence wrote:
It wasn't a conscious choice, but it would slow things down a
bit. Not
by
__
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
[[alternative HTML version deleted]]
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
Her
nder and do not
necessarily represent the views of the Babraham Institute. Full conditions at:
www.babraham.ac.uk<http://www.babraham.ac.uk/terms>
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
Her
want to do now. The change to the build system
is too big to make it 1 week before a release.
H.
Dan
- Original Message -
From: "Hervé Pagès"
To: "Dan Tenenbaum"
Cc: "bioc-devel"
Sent: Monday, October 5, 2015 4:57:38 PM
Subject: Re: zzz.R in GenoView
e field for GenoView.
- Original Message -
From: "Hervé Pagès"
To: "Dan Tenenbaum"
Sent: Monday, October 5, 2015 3:21:27 PM
Subject: zzz.R in GenoView
FYI
http://bioconductor.org/checkResults/3.2/bioc-LATEST/GenoView/linux1.bioconductor.org-buildsrc.html
Looks like zzz.R needs
ing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
[[alternative HTML version deleted]]
___
Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org>
mailing list
https://s
ternative HTML version deleted]]
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Bo
Hi Hervé,
This still looks broken in the current bioc-devel. Just wanted to
follow up in case it got missed. Thanks again.
Leonard
On Thu, Jun 11, 2015 at 11:59 AM, Leonard Goldstein wrote:
Thanks Hervé.
Best wishes,
Leonard
On Thu, Jun 11, 2015 at 10:58 AM, Hervé Pagès wrote:
Hi Leonar
xtractors don't let the user choose which column
to return at the moment so that's why it was decided (a long time ago)
to return exon internal ids *and* names (better more than less).
H.
Marc
On Tue, Sep 22, 2015 at 5:29 PM, Hervé Pagès mailto:hpa...@fredhutch.org>> wrote:
cklayer_1.29.27
[11] futile.options_1.0.0 bitops_1.0-6
[13] RCurl_1.95-4.7 biomaRt_2.25.3
[15] RSQLite_1.0.0 Biostrings_2.37.8
[17] Rsamtools_1.21.17 XML_3.98-1.3
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Ce
ation semantic ASAP. Unfortunately
this won't happen for BioC 3.2...
H.
so here the modification of txdb gets carried through to the original
object.
Best,
Kasper
[[alternative HTML version deleted]]
___
Bioc-devel@r-project.org mai
On 09/21/2015 10:39 AM, Hervé Pagès wrote:
On 09/21/2015 02:06 AM, Christian Arnold wrote:
Hi Jim, Kasper, and Hervé,
thanks a lot for the quick answer. For some reason, I was under the
impression that I have to use exactly the original prototype from the
generics, but I didn't fully re
601 - 700 of 1050 matches
Mail list logo
