Moderator: daniel.vantwisk

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Posts by daniel.vantwisk

<prev • 17 results • page 1 of 2 • next >
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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 10 weeks ago by daniel.vantwisk30
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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 3 months ago by daniel.vantwisk30
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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 3 months ago by daniel.vantwisk30
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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 3 months ago by daniel.vantwisk30
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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 3 months ago by daniel.vantwisk30
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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 Your version of R, Bioconductor, and GenomicFeatures appears to be out-of-date.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 6 months ago by daniel.vantwisk30
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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 8 months ago by daniel.vantwisk30
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Comment: C: Obsolete REFSEQ annotation
... Could you add the output of sessionInfo() to your question? ...
written 12 months ago by daniel.vantwisk30
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Answer: A: org.Hs.eg.db error same ensembl ID in different genes
... The mapping is not incorrect, but based on older resources from NCBI.  The most recent version of org.Hs.eg.db(3.4.1) was built from resources from NCBI on March 29th 2017.  We do not continuously rebuild our annotation resources so that we can allow researchers who are using these resources to get ...
written 13 months ago by daniel.vantwisk30
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Answer: A: dada2 unavailable for R 3.4.1
... It appears that your version of BiocInstaller is out-of-date.  The current release version of BiocInstaller is v1.26.0.  Try running the following code and try installing the package again: source("http://bioconductor.org/biocLite.R") biocLite("BiocUpgrade") If this doesn't work, this page conta ...
written 14 months ago by daniel.vantwisk30

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Scholar 16 months ago, created an answer that has been accepted. For A: Possible bug: outdated result from listDatabases()

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