Moderator: daniel.vantwisk

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Posts by daniel.vantwisk

<prev • 19 results • page 1 of 2 • next >
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Answer: A: makeOrgPackage Error in result_bind(res@ptr, params) : NOT NULL constraint f
... I'm not able to replicate this but the failing code in `AnnotationForge` is: message("Populating genes table:") sql<- paste(" CREATE TABLE IF NOT EXISTS genes ( _id INTEGER PRIMARY KEY, GID VARCHAR(10) NOT NULL UNIQUE -- Gene ID );") dbG ...
written 3 months ago by daniel.vantwisk50
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Comment: C: Error in .merge_transcript_parts(transcripts)
... I've tested this with a modified file (10th column removed since GFF files have 9 columns), and got the same error as you. The error is thrown by the .merge_transcript_parts() function in GenomicFeatures. In essence, tt seems the reason you are getting the error is that the tx_type value generated i ...
written 11 months ago by daniel.vantwisk50
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Comment: C: Problems with Organism.dplyr
... Thank you for posting about this issue.  Any criticism about the package is helpful.  It allowed Martin and I to discuss and make a few small changes that needed to be made. ...
written 14 months ago by daniel.vantwisk50
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Answer: A: makeTxDbFromGFF error "stop codons that cannot be mapped to an exon"
... I've been looking through this case, more particularly at the function .find_exon_cds() that is a level higher than .reject_transcripts(), the function that is throwing the warning. In this function, it undergoes a process of finding overlaps between the exons and stop_codon sequences, in particula ...
written 15 months ago by daniel.vantwisk50
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Answer: A: an error in BioMart regarding gene annotations
... Martin Morgan and I looked into the issue today and it seems to be a problem on UCSC's end.  There seems to be an issue with mapping between UCSC's knownGene and LocusLink (i.e. the knownToLocusLink table) that can map two separate genes to the same Entrez gene IDs.  For example, SMIM11A and SMIM11B ...
written 15 months ago by daniel.vantwisk50
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Answer: A: TxDb basic question
... It appears that the transcript_nrow is correct.  This link points us to the RefSeq Genes table from UCSC: https://genome.ucsc.edu/cgi-bin/hgTables?db=rheMac8&hgta_group=genes&hgta_track=refGene&hgta_table=refGene&hgta_doSchema=describe+table+schema Given each row in the table accou ...
written 15 months ago by daniel.vantwisk50
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Comment: C: Error: vector memory exhausted (limit reached?)
... What package is SCseq() from?  Is it a Bioconductor package?  It may be helpful to add the package that is from in the tags so people who are knowledgeable about the package can assist you.   ...
written 16 months ago by daniel.vantwisk50
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Comment: C: Setting up PLAYRDesign gives error on makeTxDbFromUCSC, error in tableNames
... Your version of R, Bioconductor, and GenomicFeatures appears to be out-of-date.  Updgrading your version of R to the current release and following the instructions to update Bioconductor may solve the issue. ...
written 18 months ago by daniel.vantwisk50
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Comment: C: GO.db failure to install
... It seems that this issue is related to your environment and not GO.db or R.  I'm not able to reproduce this error since it involves your computing environemnt, but as per this article: https://support.rstudio.com/hc/en-us/articles/203775903-Fixing-startup-error-where-manipulate-and-rstudio-packages- ...
written 20 months ago by daniel.vantwisk50
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Comment: C: Obsolete REFSEQ annotation
... Could you add the output of sessionInfo() to your question? ...
written 24 months ago by daniel.vantwisk50

Latest awards to daniel.vantwisk

Scholar 2.3 years ago, created an answer that has been accepted. For A: Possible bug: outdated result from listDatabases()

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