User: Marc Carlson

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Marc Carlson7.2k
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Posts by Marc Carlson

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Answer: A: Gene Ontolology and Annotation
... Hi, So James is right about the GO.db data being the place where the gene ontology data is stored.  If you are interested in the GO to gene mappings represented in the org.Sc.sgd.db and org.Hs.eg.db packages.  For the org.Hs.eg.db package, those data came from here: > org.Hs.eg.db OrgDb object: ...
written 4.5 years ago by Marc Carlson7.2k
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Answer: A: Mapping of two different regions to one gene symbol
... Your question is a little bit opaque to me.  But it is pretty normal for a couple of different ranges to overlap with a single gene.  Can you please clarify what it is you are trying to do?    Marc ...
written 4.5 years ago by Marc Carlson7.2k
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Answer: A: Setting package name in makeTxDbPackage
... Actually Keith, I am trying to move things towards a world where these resources can just come down from the AnnotationHub.  So for example you can already do this: library(AnnotationHub) ah = AnnotationHub() ahs = subset(ah, ah$rdataclass=='OrgDb') Which already has about ~1100 OrgDb objects in ...
written 4.5 years ago by Marc Carlson7.2k
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Answer: A: Setting package name in makeTxDbPackage
... Hi Keith, I recognized the potential for that problem I just wasn't sure if it was actually happening to people out in the real world or not (most people still only work on mouse and humans).  And this is why I was mentioning the taxonomyId argument.  Because especially for bacteria, the tree at NC ...
written 4.5 years ago by Marc Carlson7.2k
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Comment: C: Setting package name in makeTxDbPackage
... Hi Diego, I would rather that you use only official organism names as it creates confusion if you use ones that are not.  I just updated our taxonomy data for this purpose and after I check it in (this morning) you will have this 'official' list of names to choose from: 5861 Pl ...
written 4.5 years ago by Marc Carlson7.2k
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Answer: A: Setting package name in makeTxDbPackage
... OK Diego, I have checked in a change to devel that should allow you to proceed.  But I could use more information from you as I can't test your specific case since you didn't give me enough information to fully reproduce it this...  :/ Also for some of your other species names like "Plasmodium yoel ...
written 4.5 years ago by Marc Carlson7.2k
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Answer: A: Setting package name in makeTxDbPackage
... There is a function deep down that generates the name from (among other things) the genus and species information provided.  Right now a major goal of that function was to produce consistent names, but it seems that we should probably nudge that towards greater specificity instead.  I will look into ...
written 4.5 years ago by Marc Carlson7.2k
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Answer: A: gene model generation support?
... I like this suggestion Vince.  There is another high level function that I recently added to OrganismDbi and which I think could be a good complement to something quite close to this.  I plan to explore this some more when I work on enhancing the other function. ...
written 4.5 years ago by Marc Carlson7.2k
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Answer: A: Faulty entry in org.Hs.eg.db, a force check perhaps?
... You are correct that the data is just coming to us like that from NCBI.  http://www.ncbi.nlm.nih.gov/gene/?term=100131205 You are also correct that I *could* easily filter out all IDs that don't start with 'ENS'.  And if I did that process, it would only remove that single goofy entry...  librar ...
written 4.6 years ago by Marc Carlson7.2k
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Comment: C: Secondary accession lookup with UniProt.ws
... Yes.  This is unfortunate, but unless UniProt sees fit to actually allow me to use the IDs to look up actual information, then it doesn't really matter what they are called.  :( Also problematic is the fact that the UniProt site is a very large resource and is not extremely fast as a result.  I sus ...
written 4.6 years ago by Marc Carlson7.2k

Latest awards to Marc Carlson

Popular Question 3.3 years ago, created a question with more than 1,000 views. For Google hangout on Wed December 10th for new package authors
Popular Question 3.3 years ago, created a question with more than 1,000 views. For how to get gene list for given GO terms?
Scholar 4.2 years ago, created an answer that has been accepted. For A: Installation of TxDb.Hsapiens.UCSC.hg19.knownGene fails.
Teacher 4.8 years ago, created an answer with at least 3 up-votes. For A: Installation of TxDb.Hsapiens.UCSC.hg19.knownGene fails.
Scholar 4.8 years ago, created an answer that has been accepted. For A: Installation of TxDb.Hsapiens.UCSC.hg19.knownGene fails.
Autobiographer 5.2 years ago, has more than 80 characters in the information field of the user's profile.
Centurion 5.2 years ago, created 100 posts.

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