User: Malcolm Cook

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Malcolm Cook1.5k
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Posts by Malcolm Cook

<prev • 174 results • page 1 of 18 • next >
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Comment: C: Yeast org.Sc.sgd.db lacks SYMBOL - should it have one? - how to make it interope
... I'd argue that how to obtain the "names" of the genes was not my original question at all. But thanks for your original help. I posted my own "workaround" as a solution, below. ...
written 5 weeks ago by Malcolm Cook1.5k
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Answer: A: Yeast org.Sc.sgd.db lacks SYMBOL - should it have one? - how to make it interope
... I found someone similarly afflicted who reported the issue as [enrichPathway make readable does not work for yeast genome](https://github.com/GuangchuangYu/ReactomePA/issues/12) - this prompted further sleuthing on my part which resulted in [more understanding and a **workaround**][1]: "translate my ...
written 5 weeks ago by Malcolm Cook1.5k
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Comment: C: Bug in makeOrgPackageFromNCBI from AnnotationForge?
... Marc, I find this to still be the state of affairs and wonder if you have any suggested alternative approaches. For example, there are only 36 rows of `gene_info` in the org.Scerevisiae.eg.db, forged as follows: makeOrgPackageFromNCBI( version = "0.0.1" ,outputDir = "test" ,tax ...
written 6 weeks ago by Malcolm Cook1.5k
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Comment: C: Yeast org.Sc.sgd.db lacks SYMBOL - should it have one? - how to make it interope
... Thanks, but... I am able to run `enrichGo(readable=FALSE, OrgDb=org.Sc.sgd.db, ...)` However, I would further like to use `clusterProfiler::cnetplot` and have the nodes labelled not with the ENTREZID which I understand requires me to have passed `readable=TRUE`. I am looking for suggestions tha ...
written 6 weeks ago by Malcolm Cook1.5k
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Yeast org.Sc.sgd.db lacks SYMBOL - should it have one? - how to make it interoperate with clusterProfiler in its absence?
... library `org.Sc.sgd.db` lacks a SYMBOL attribute and instead has COMMON and GENENAME As a result, it does not interoperate with the clusterProfiler package when using the `readable=TRUE` option (without which genes are labelled by their ENTREZID, which is relatively uninformative). clusterProfiler ...
annotation go clusterprofiler org.sc.sgd.db written 6 weeks ago by Malcolm Cook1.5k
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Comment: C: GenomicFeatures supportedUCSCFeatureDbTracks never returns and has to be termina
... The code underlying supportedUCSCFeatureDbTracks is > supportedUCSCFeatureDbTracks function (genome)  {     session <- browserSession()     genome(session) <- genome     query <- ucscTableQuery(session)     trx <- trackNames(ucscTableQuery(session))     supported <- makeWhiteList( ...
written 4 months ago by Malcolm Cook1.5k
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Comment: C: GenomicFeatures supportedUCSCFeatureDbTracks never returns and has to be termina
... Thanks, James, but I don't understand your response.  I commented on the function supportedUCSCFeatureDbTracks, which by my sights you did not exercise in your code, so, how could it address my issue? ...
written 4 months ago by Malcolm Cook1.5k
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GenomicFeatures supportedUCSCFeatureDbTracks never returns and has to be terminated with C-c
... In my hands, supportedUCSCFeatureDbTracks never returns and has to be terminated with C-c. Any debugging help very welcome. I've tried with hg19 in addition to dm6.  Below I report my linux setup, but it also fails under windows, R 3.5.1, GenomicFeatures_1.34.1 >  trks<-supportedUCSCFeature ...
genomicfeatures bug written 4 months ago by Malcolm Cook1.5k • updated 4 months ago by James W. MacDonald49k
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Comment: C: Reorder exons on negative strand in GRanges list
... Mike - thanks for offering to take a look, and even more so for the "spot on" comment about using flank... you're absolutely right, computing flanking.grl as below is ~100x faster           up.gr<-trim(flank(intron.gr,flankSize,T))         down.gr<-trim(flank(intron.gr,flankSize,F))         ...
written 6 months ago by Malcolm Cook1.5k
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Comment: C: Reorder exons on negative strand in GRanges list
... Here's timing produced by the five statements in the following function, to give you a sense of relative speed on my computer:    user  system elapsed   12.227   0.871  13.100     user  system elapsed   41.688   3.735  45.423     user  system elapsed  636.549  29.291 665.827     user  system elapse ...
written 6 months ago by Malcolm Cook1.5k

Latest awards to Malcolm Cook

Scholar 23 months ago, created an answer that has been accepted. For A: Importing a .txt file with multiple headers into R
Popular Question 4.0 years ago, created a question with more than 1,000 views. For Is Bioconductor 3.0 compatible with R 3.1.2?
Scholar 4.0 years ago, created an answer that has been accepted. For A: Importing a .txt file with multiple headers into R
Centurion 13.7 years ago, created 100 posts.

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