Hi Michael, Herve,
On 6/17/2015 9:43 PM, Hervé Pagès wrote:
Hi Michael,
On 06/17/2015 12:35 AM, Michael Love wrote:
Background:
With previous approaches that I would recommend to users for building
txdb along the way of making count tables, it was desirable that the
GTF release information wo
Hi everyone,
Files from Epigenomics RoadMap Project[1] have been added to AnnotationHub.
This vignette[2] inside AnnotationHub gives you a quick tour on how to
access these files via the Hub with some examples.
Please let us know if you'd like any other files to be added to the Hub
from the
nks and Regards,
Sonali.
On 12/8/2014 8:44 AM, Vincent Carey wrote:
On Mon, Dec 8, 2014 at 11:22 AM, Sonali Arora wrote:
Hi Vince,
On 12/8/2014 7:38 AM, Vincent Carey wrote:
Very nice. Is "WholeGenomeData" under "SequencingData" sufficiently
clear?
We mirrored
Thanks for joining us today for the Webinar!
For those who missed it today, a video recording is now available at :
https://www.youtube.com/watch?v=QfqaK_BHebU
Thanks and Regards,
Sonali.
On 12/9/2014 11:49 AM, Sonali Arora wrote:
Hi everyone,
Please be reminded that we are inviting you to
Hi everyone,
Please be reminded that we are inviting you to join a webinar
tomorrow(Dec 10th, 2014) at 8:00AM PST.
You can "tune in" at: http://youtu.be/QfqaK_BHebU
Please feel free to chat and ask questions, they will be collectively
answered at the end of a short presentation.
A recordin
Original Message
Subject:Re: Experiment Data biocViews updates
Date: Mon, 08 Dec 2014 15:43:52 +
From: Joseph Nathaniel Paulson
To: Sonali Arora
Hi Sonali,
Hope all is going well. I saw the new data biocViews for the experiment
data. I was wonder
Hi everyone,
We have revised the Experiment Data biocViews and have updated most of the
Experiment Data packages using our word lookup function(
recommendBiocViews() ) .
Package Authors are encouraged to check the new biocViews added to their
Experiment Data package and add more relevant ones f
Just an update, we have updated the vignette "Submitting your Organism
to GenomeInfoDb" with contact information.
Please send all subsequent "organism" requests to
"maintai...@bioconductor.org"
Thanks,
Sonali
On 10/22/2014 9:10 AM, Sonali Arora wrote:
Hi Leo,
Y
Hi Leo,
This bug is now fixed .
JGI2 was being incorrectly returned previously.
The correct style is JGI2.F and from now on, it will always check only
for JGI2.F
> library(GenomeInfoDb)
> seqlevelsStyle("T")
[1] "JGI2.F"
> seqlevelsStyle("LGI")
[1] "NCBI"
> mapSeqlevels('LGI', 'JGI2.F')
[1] "T
Hi Leo,
To summarize, These are the concerns raised in your previous email :
*a) mapSeqlevels() should return current style along with other mapped
styles? **
look at extendedMapSeqlevels()
*I am looking into this. I have a few thoughts/ questions for you.
The main idea of mapSeqlevels() is to
Hi Leo,
You can contact me for adding a specific organism to GenomeInfoDb.
I'll talk with the team and update the vignette.
Thanks
Sonali.
On 10/21/2014 8:53 PM, Maintainer wrote:
Hello,
As you can see in https://support.bioconductor.org/p/62136/#62180 the
GenomeInfoDb vignette for adding an
Hi Levi,
I'll correct the spelling in biocViews and ask the authors of
SomaticSignatures to do the same.
It will be "PrincipalComponent"
It might take a day or two to reflect on the website though.
Thanks for bringing it to our attention,
Sonali.
On 9/18/2014 10:54 AM, Levi Waldron wrote:
"
your DESCRIPTION file.
b) If the video for your package already lives on youTube or your
website - just add the permanent link in
the Video : tag of your DESCRIPTION file.
--
Thanks and Regards,
Sonali Arora
___
Bioc-devel@r-project.org mailing list
Hi everyone,
Initially the keepStandardChromosomes required users to specify 3 arguments
( the Seqinfo object, the species and the Style)
I have now implemented it to work only on the Seqinfo object. (A species
argument can be specified
optionally ) Hope that helps.
>gr <- GRanges(c("chr1", "ch
Hi Micheal ,
I updated the code for renameSeqlevels yesterday in response to a test case.
From the function -
level <- seqlevels(x)
idx <- match(nms,level)
idx <- idx[complete.cases(idx)]
value <- replace(level,idx , value[1:length(idx)])
It is still matching nms (names(value) ) and level ( s
Hi Martin,
I have fixed this warning issue yesterday - you do not need to do
anything about it.
Thanks
Sonali.
On 4/1/2014 1:32 AM, Martin Rijlaarsdam wrote:
Dear list,
I had the same thing with a package that is currently under submission
(DMRforPairs).
Thanks,
Martin
--
M.A. (Martin) R
Hi Mark,
I have fixed this warning issue yesterday - you do not need to do
anything about it.
Thanks
Sonali.
On 4/1/2014 1:29 AM, Mark Dunning wrote:
Hi all,
I am seeing a warning in the check report for beadarray which seems to
relate something in GenomicRanges (which I am importing). Shou
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