User: Malcolm Cook

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Malcolm Cook1.5k
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Posts by Malcolm Cook

<prev • 175 results • page 1 of 18 • next >
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Answer: A: Filtering GFF3 file
... Three passes should do it easily. First: Use perl to find lines matching "Note=" and to build new regular expressions based on the value of their ID. Then: Use those regular expressions to grep for lines containing (or not) the new regular expressions. ``` perl -n -e 'print "ID=$1\\W\n" if m/ID=( ...
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
... 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 7 months 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 7 months 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 7 months 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 7 months 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 7 months 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 10 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 10 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 10 months ago by Malcolm Cook1.5k • updated 10 months ago by James W. MacDonald51k
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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 12 months ago by Malcolm Cook1.5k

Latest awards to Malcolm Cook

Scholar 2.5 years ago, created an answer that has been accepted. For A: Importing a .txt file with multiple headers into R
Popular Question 4.5 years ago, created a question with more than 1,000 views. For Is Bioconductor 3.0 compatible with R 3.1.2?
Scholar 4.5 years ago, created an answer that has been accepted. For A: Importing a .txt file with multiple headers into R
Centurion 14.2 years ago, created 100 posts.

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