', I get
>
> custom_anno/script/bindb.sql
> 328:INSERT INTO pfam
>
> pfam/script/srcdb_pfam.sql
> 202:-- INSERT INTO pfamb
>
> organism_annotation/script/bindb_yeast.sql
> 441:-- INSERT INTO pfam
>
> yeast/script/bindb.sql
> 241:-- INSERT INTO pfam
>
> The
Hi Jim,
You asked me on Friday where the PFAM Ids for yeast came from and I
couldn't recall because at the moment I was at Seattle Childrens (and thus
nowhere near my copy of my source code). But I also said I would look into
it for you later (and I have). Here is what my code tells me: So ever
Works for me.
Marc
On Tue, Sep 22, 2015 at 6:03 PM, Hervé Pagès wrote:
> Hi Marc,
>
> On 09/22/2015 05:39 PM, Marc Carlson wrote:
>
>> Herve is right. UCSC doesn't give us this information, And actually, I
>> think it's pretty rare to see exon names from
Herve is right. UCSC doesn't give us this information, And actually, I
think it's pretty rare to see exon names from anybody. So it's weird to
me that they are a default return value for this method.
Marc
On Tue, Sep 22, 2015 at 5:29 PM, Hervé Pagès wrote:
> Hi Sonali,
>
> UCSC doesn't pro
Hi Arne,
So this time when I look at the bioc-devel email list, I don't see a
record for this last name (or this email). In fact the only way I could
be sure it was you was that your post was the same... ;) If you want to
post from gmail, then you will need to subscribe the gmail address to
ssage is objectionable to some, you could give the option
> for people to set a global flag to shut it off. Something like
>
> if(!pleaseMakeItStop)
> message()
>
> and they could set
>
> pleaseMakeItStop = TRUE in their .Rprofile
>
> Is that a reasonable compromise?
>
Hi Jim,
I do agree that the warning was protective for that (this is why I put
it there).
But it was also annoying for many and a source of some confusion because
when people see a warning() they think that something has gone wrong
with the code that was just run. And in this case the selec
he seqinfo available in the GRanges as mentioned
> in my previous mail. In the meantime I'll try to fetch the chrom
> lengths myself but would be nice to have all that ready in the GRanges
> at some point.
>
> cheers, jo
>
>> On 11 Apr 2015, at 00:54, Marc Carlson
On 04/10/2015 12:18 PM, Rainer Johannes wrote:
> dear Sonali, Herve,
>
> On 10 Apr 2015, at 19:59, Herv� Pag�s
> mailto:hpa...@fredhutch.org>> wrote:
>
> Hi Johannes, Sonali,
>
> On 04/10/2015 09:40 AM, Arora, Sonali wrote:
> Hi Rainer,
>
> Just to be clear - what do you want to be available from
This is done BTW.
Marc
On 02/27/2015 02:43 PM, Marc Carlson wrote:
Hi Sean,
This seems like a solid suggestion. I have put it into my queue.
Marc
On 02/27/2015 04:41 AM, Sean Davis wrote:
Hi, Marc.
Since Ensembl has switched to GRCh38 for their most recent builds, to
get
access to
other 'ORF'
used in resources from SGD (which this has nothing to do with since the
data all comes from plasmoDB).
Anyhow, I have fixed the software bugs and pushed a patch to release and
devel. It should be up in about a day.
Marc
On 03/18/2015 10:23 AM, Marc Carlson wrote:
Hi Paolo
Hi Paolo,
The ORF type has never been available for that package. This is a bug
in the columns method (which I will now fix). Thanks for reporting it.
Marc
On 03/18/2015 03:00 AM, Paolo Martini wrote:
Dear Bioconductor,
I am working with the annotation package "org.Pf.plasmo.db".
I tr
Hi Sean,
This seems like a solid suggestion. I have put it into my queue.
Marc
On 02/27/2015 04:41 AM, Sean Davis wrote:
Hi, Marc.
Since Ensembl has switched to GRCh38 for their most recent builds, to get
access to GRCh37 data now requires a different host and port for biomaRt.
These are
Hi Vince,
First of all thank you for using OrganismDb objects. You raise some
interesting points though about keeping these APIs better synchronized
that I feel point to some deficiencies in the current design. I spoke
with Herve about this and we are puzzling over possibly using
inheritanc
Hi Avinash,
So the argument for the importance of reproducible research *definitely*
resonates with us here as it is a major goal of ours. However while the
decision to use the same library as your paper helps to make the
immediate work more reproducible, it simultaneously hampers others from
Hi Peter,
I would add that you can see a listing all the currently
pre-manufactured TxDb packages here:
http://www.bioconductor.org/packages/devel/BiocViews.html#___TxDb
And for convenience you can also use an OrgansimDb package to connect
the contents of the TxDb package with the older org
Thanks Vince,
But actually I was planning to take this straight to the manual pages.
It's going to make for a longer manual page, but someone might find it
helpful down the line.
Marc
On 12/05/2014 10:14 AM, Marc Carlson wrote:
Hi Jelle,
Thank you for your patience in waiting f
Hi Jelle,
Thank you for your patience in waiting for my answer here. It took me a
lot longer to properly test and validate this than I initially expected.
So if you look at amigo you can see these graph views that show you what
the current terms up and downstream of a given GO term should be
Hello new package authors,
Based on the number of new software packages being submitted to the
project it seems that Bioconductor is more popular than ever. Last
release we added a hundred and ten new packages (a new record).
A lot of the popularity of this project is because Bioconductor pa
Hi Raffaele,
You are in luck today because while we normally do *not* have mechanisms
to harmonize the non-standard chromosome names, for this specific case
Herve wrote some code to handle it. So you want to look at this:
library(GenomeInfoDb)
?fetchExtendedChromInfoFromUCSC
Marc
On 12
Hi Robert,
I am sending you another invite now.
Marc
On 10/16/2014 08:59 AM, Valerie Obenchain wrote:
Hi Robert,
Annotation packages are generally updated before each release. You
should have received an email from Marc (cc'd) last month asking if
you had any updates. Updated packages are
Actually they are required in one sense. Just not required of an end
user who would be calling the function (so not for that manual page).
But they are required in a separate internal sense (which is what the
error is referring to) and that is that the database that is loaded it
must contain
Hi Raffaele,
This problem should be resolved in devel at this time. Please update to
the latest version of AnnotationDbi (1.27.14) and try again.
Marc
On 09/23/2014 02:36 PM, calogero UNITO wrote:
affaeleaffaeleHi Vincent,
I have further investigated the error I have in the vignette of c
through
> TxDb.
>
> On Mon, Sep 22, 2014 at 8:38 PM, Marc Carlson <mailto:mcarl...@fhcrc.org>> wrote:
>
> Hi Vince,
>
> So if you wanted to do this manually, then the thing you would
> want to do is to get a gene ID from the probe and to take that to
Hi Vince,
So if you wanted to do this manually, then the thing you would want to
do is to get a gene ID from the probe and to take that to a TranscriptDb
object (again: that is if you wanted to do it manually). Alternatively,
if you had an OrganismDb object then this association would be hand
Hello package contributors,
Please note that next Thursday is the deadline for submitting new
packages if you want them to make it into the upcoming October release.
You can see the release schedule here:
http://www.bioconductor.org/developers/release-schedule/
Please also take note of the
Hello,
This is a second warning that in less than a week we plan to roll out
the new support site for Bioconductor.
*Important* Once the support site is 'live', posts to the Bioconductor
mailing list will receive an automatic reply indicating that it is no
longer in service and directing you to
Hello,
Thank you to those who have participated in the Beta for our new
support site. The beta period is now over, and we are getting ready
for a formal launch of the site during the week of September 15th.
*Important* Once the support site is 'live', posts to the Bioconductor
mailing list will
rs get help faster, since those of us who
are not constantly watching the mailing list will see relevant
questions right away.
Stephanie
On 8/18/14 12:15 PM, Marc Carlson wrote:
Hello!
This is a message to announce the beta test for our new support site.
We hope to replace the regular Biocond
ot just a copy and paste (fork)
of biostars ( I have nothing against biostars btw)
That's my personal opinion of course :)
Rad
On Aug 18, 2014, at 12:15 PM, Marc Carlson wrote:
Hello!
This is a message to announce the beta test for our new support site.
We hope to replace the regular B
Hello!
This is a message to announce the beta test for our new support site.
We hope to replace the regular Bioconductor mailing list with this
site soon and we have imported the past 11+ years of mailing list
discussion into this new site. If you would like to help us test it
out you can do tha
Hi Vince,
The current Homo.sapiens package/object contains a reference to an hg19
TranscriptDb object (which makes it specific to hg19). But you can
easily make a custom Homo.sapiens object of your own that points to a
custom TranscriptDb object. Making a custom OrganismDbi object is easy
t
Hi Michael,
The fact that duplicate keys are not being allowed in OrganismDb objects
is an inconsistency that I will be looking into. That is, if you do the
same thing with orgDb or TranscriptDb objects, duplicates are allowed
and passed along. So I plan to fix this. I have checked in a
pre
Hi everyone,
As many of you already know we have long provided organism annnotation
packages that give gene based annotations for selected organisms. And
we intend to keep doing that. But these days there is also a lot of
other data at NCBI that could be used to make gene based databases for
Hi,
I just wanted to apologize for some spam that was sent by a process I
was testing. If you have received any strange spam from
biocbu...@fhcrc.org this is an accident and you can ignore or delete it.
Marc
___
Bioc-devel@r-project.org mailing l
On 03/12/2014 02:53 PM, Marc Carlson wrote:
I just checked a fix in for this bug to GenomicFeatures (which happens
to be where the problem was). It should percolate out to the build
system soon.
Marc
On 03/12/2014 02:19 PM, Servant Nicolas wrote:
Hi guys,
Thanks for your feedbacks.
Ind
t;EXONNAME" "EXONCHROM" "EXONSTRAND"
[11] "EXONSTART" "EXONEND""GENEID" "TXID" "EXONRANK"
[16] "TXNAME" "TXCHROM""TXSTRAND" "TXSTART""TXEND"
I will mo
Thanks Nicolaus! That's a good bug. I will work on a fix. The reason
why James work-around here functions is because the number of databases
that it has to query is fewer by one. It is also faster for this
reason. So when you say GENEID you mean the ids used in the associated
txdb database
Hi Julian,
This is a complicated issue for us and we have to choose our next move
carefully since we don't have unlimited resources. Especially not with
respect to time. But I wanted to let you know that we appreciate your
comment and that we are still thinking about it.
Marc
On 10/10/
Hello everyone,
This is a courtesy message to remind all package developers that next
Wednesday the 9th of October is the deadline for all packages to pass
the build system without any errors or warnings.
Please have a look at our build system for the development branch and
make sure that th
objects?
That would make seqlevels<- a little bit more user-friendly on
those objects.
Thanks,
H.
On 09/13/2013 10:38 AM, Marc Carlson wrote:
Hi Florian,
Yes we are trying to make things more uniform. seqlevels() lets you
rename as well as deactivate chromosomes you want to ignore, so it was
re
er_1.0-5
> [16] RCurl_1.95-4.1 rpart_4.1-3 Rsamtools_1.13.39
> [19] RSQLite_0.11.4 rtracklayer_1.21.11 scales_0.2.3
> [22] stats4_3.0.1stringr_0.6.2 tools_3.0.1
> [25] XML_3.98-1.1zlibbioc_1.7.0
>
>
>
> From: Marc Carlson mailto:mcarl...@fhcrc.
gt; Kasper
>
>
> On Thu, Sep 12, 2013 at 1:22 PM, Marc Carlson <mailto:mcarl...@fhcrc.org>> wrote:
>
> Hi Kasper,
>
> You should get an email from me in the coming weeks with
> instructions regarding the upcoming release. If you need
> somethin
Hi Florian,
Yes we are trying to make things more uniform. seqlevels() lets you
rename as well as deactivate chromosomes you want to ignore, so it was
really redundant with isActiveSeq(). So we are moving away from
isActiveSeq() just so that users have less to learn about. The reason
why is
Hi Kasper,
You should get an email from me in the coming weeks with instructions
regarding the upcoming release. If you need something changed before
then, please send me an email.
Marc
On 09/11/2013 06:17 PM, Dan Tenenbaum wrote:
Annotation packages are not in svn. Send your changes
On 08/08/2013 07:00 PM, Dario Strbenac wrote:
It's not documented by ?loadDb, but providing an absolute path doesn't work,
and shows an unusual error message.
genes17 <- loadDb("/nb/dario/genes/gencode17.db")
Error in loadDb(file, dbType, dbPackage, ...) :
error in evaluating the argument
Hi Carles,
In general there are three steps to consider in turn:
1) Look at the repository of experiment data packages. If there are
existing packages there with data that you can use then you probably
want to use those.
2) Look for ways to make the data smaller and still get your
testing/ex
is easy yet to get the gene symbols returned as a
> result of e.g. a transcripts() or exons() call?
>
> Michael
>
>
> On Tue, Apr 30, 2013 at 2:16 PM, Marc Carlson <mailto:mcarl...@fhcrc.org>> wrote:
>
> Related to this:
>
> I have added getters for seq
Related to this:
I have added getters for seqinfo (and friends) for the OrganismDb
objects. I have not added the setters yet though since that requires
some refactoring of what an OrganismDb object actually is internally.
But I intend to do this also.
Marc
On 04/25/2013 09:32 AM, Vale
Hello everyone,
This year Bioconductor is participating in the Google Summer of Code.
Interested parties can see our GSOC page here:
https://google-melange.appspot.com/gsoc/org/google/gsoc2013/bioconductor
Also, we know that we only have a few ideas on our ideas list this year.
It's because we
Hi Mattia,
These packages are actually modular and are intended to be adjustable if
you need to use other TxDbs. Please see the main package vignette for
OrganismDbi for details on how this works.
http://www.bioconductor.org/packages/2.12/bioc/vignettes/OrganismDbi/inst/doc/OrganismDbi.pdf
Hello everyone,
If you are planning to submit a package to the project in time for the
upcoming release, please be sure to do so by next Wednesday (the 13th).
You can see the deadline in our release schedule here:
http://www.bioconductor.org/developers/release-schedule/
Thanks again,
M
Hi Davide,
Lots of good advice here. The main goal with two packages is to
minimize dependencies for the experiment data package as this is
presumed to be the less specialized package. Whenever you have a
package ready please be sure to follow the follow the instructions on
the link that He
look like our
annotation again.
Marc
On 02/12/2013 01:35 PM, Marc Carlson wrote:
On 02/12/2013 10:04 AM, Tim Triche, Jr. wrote:
re: '[BioC] question about Gviz' thread fallout:
Yesterday I rolled a relatively simple programmatic way to label UCSC
KnownGene entries with the
On 02/12/2013 10:04 AM, Tim Triche, Jr. wrote:
> re: '[BioC] question about Gviz' thread fallout:
>
> Yesterday I rolled a relatively simple programmatic way to label UCSC
> KnownGene entries with their symbols. However, some isoforms (e.g. some
> for NRIP1 and CDKN2B) seem to be missing from the
Hi Malcolm,
Not too much that hasn't been mentioned before. So I bet that many
people can probably walk past this one.
Both GFF and GTF files have many of the same things that come up when
you use them. They both are being used for things today (like
transcriptomes) which represent a prett
column manually and specify them in the function of
> 'makeTranscriptDbFromGFF'.
>
> btw, Is this required? It looks like the GenomicFeatures trying to
> infer exon rank if I didn't provide that information, so I thought
> 'exonRankAttributeName' is optional
Hi Malcolm,
In general I have found ensembl to be really great and I expect that
their gtf files are probably fine. Usually the exon rank is the 1st
thing you will see left out when a gtf file is cutting corners, and you
are correct that they seem to be including that. I ran the one for Homo
Hi Tengfei,
Yes that looks like an oversight. Thanks for reporting that! I will
extend makeTxDbPackage so that it's more accommodating of these newer
transcriptDbs. If you want to help me out, you could call saveDb() on
your gmax189 object and send me the .sqlite file that you save it to.
That makes sense since this metadata table is the very 1st thing that
will be looked at when R wants to make an object. So when you have a
bad .sqlite file and that table is missing or unreadable this is also
the error you will see.
Marc
On 01/20/2013 07:59 PM, Dario Strbenac wrote:
It
Hi Dario,
This kind of error probably means that whatever is in your
transcriptsHs19.db database is missing a metadata table with appropriate
fields filled out. In particular, there needs to be a field (in
metadata) to define the "Db type" and also one to define the "Supporting
package". Th
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