User: rubi

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rubi70
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Posts by rubi

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Comment: C: Getting error using GenomicRanges::setdiff
... Right, sorry about that and thanks a lot for the help. ...
written 3 months ago by rubi70
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Comment: C: Getting error using GenomicRanges::setdiff
... Thanks a lot.   This, however, returns also the introns. Is it possible to get only the UTRs or to systematically remove the introns? ...
written 3 months ago by rubi70
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Getting "negative length vectors are not allowed" error in BSgenome::getSeq
... Hi,   I'm trying to retrieve the sequences of a certain transcript represented as a GenomicRanges object.   Here's the data.frame of that transcript: > exon.df         seqnames   start     end strand NW_004624885.1 3278632 3279702      + NW_004624885.1 3280386 3280638      + NW_004624885.1 3 ...
bsgenome getseq written 3 months ago by rubi70 • updated 3 months ago by Martin Morgan ♦♦ 20k
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Getting error using GenomicRanges::setdiff
... Hi,   I'm trying to use GenomicRanges::setdiff and getting an error: Error in validObject(.Object) : ))   invalid class “XIntegerViews” object: undefined class for slot "elementMetadata" ("DataTable_OR_NULL")For example, exon.df <- data.frame(seqnames=rep("chr1",12),id=c(rep("id1",4),rep("id2 ...
genomicranges setdiff written 3 months ago by rubi70 • updated 3 months ago by Michael Lawrence9.8k
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Extracting UTRs from exon and CDS data
... Hi, I have a data.frame of exons per each transcript and another, corresponding, data.frame of the cds intervals: exon.df <- data.frame(id=c(rep("id1",4),rep("id2",3),rep("id3",5)), start=c(10,20,30,40,100,200,300,1000,2000,3000,4000,5000), end=c(15, ...
genomeintervals genomicranges exons cds utrs written 3 months ago by rubi70 • updated 3 months ago by Michael Lawrence9.8k
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Comment: C: Does fgsea order the stats argument?
... Hi @assaron,   I think it's a matter of preference what you want your enrichment analysis to pick up on. Sorting only by effect size ignores the error of the estimate (qhich can often be large in gene expression data), whereas sorting by p-value does not, so I'd prefer sorting first by p-value and ...
written 3 months ago by rubi70
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Answer: A: Does fgsea order the stats argument?
... Yes. And least I think it would be helpful to have an argument that allows specifying whther stats should be sorted or not. ...
written 5 months ago by rubi70
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Does fgsea order the stats argument?
... Hi,   Does fgsea order the stats argument? What I'm currently doing is order ordering the effect (i.e. log treatment vs. control fold-changes) but their p-vaiues and passing that to fgsea. But the fgsea code suggests it re-ranks stats so the p-value ranking is lost. Is that the case? and if so is ...
fgsea written 5 months ago by rubi70
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Exporting a GenomicRanges object as GTF/GFF file
... Hi,   I'm trying to export a GenomicRanges object as a GTF file using rtrackleyr's export: Here's an example GTF file downloaded from: ftp://ftp.ensemblgenomes.org/pub/release-32/bacteria//gtf/bacteria_90_collection/_chrysanthemum_coronarium_phytoplasma/_chrysanthemum_coronarium_phytoplasma.ASM ...
rtracklayer genomicranges gff export gtf written 5 months ago by rubi70
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Getting Internal Server Error when trying to use Gviz's IdeogramTrack
... Hi, I'm using Gviz's IdeogramTrack from my institution's cluster (IdeogramTrack(genome="mm10",chromosome="chr1")). When I try this from the master node it works fine but when I try this from any other node in the cluster which IO's through the master node, it hangs and eventually I get the error me ...
gviz ideogramtrack written 9 months ago by rubi70 • updated 9 months ago by florian.hahne@novartis.com1.5k

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Supporter 9 months ago, voted at least 25 times.

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