User: rubi

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rubi90
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Posts by rubi

<prev • 48 results • page 1 of 5 • next >
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Using HDF5Array writeHDF5Array for a large dgCMatrix
... Hi, I have a large sparse matrix (40,000 by 40,000, called mat) as a dgCMatrix which I would like to save to an HDF5 file. The conversion of the dgCMatrix to an array (arr <- as(Matrix::as.matrix(mat),"HDF5Array")) is very slow and then writing the array to the HDF5 file, using:  writeHDF5Array ...
hdf5array dgcmatrix written 24 days ago by rubi90 • updated 22 days ago by Aaron Lun19k
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Answer: A: getGEO error when trying to download a series matrix file
... Thanks a lot ...
written 5 weeks ago by rubi90
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Comment: C: Does fgsea order the stats argument?
... Yep, that's exactly what I'm doing. ...
written 5 weeks ago by rubi90
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getGEO error when trying to download a series matrix file
... Hi, I'm trying to use GEOquery's getGEO for downloading the series matrix file of several studies using their GEO accessions, from my linux cluster. I originally tried: geo.accession <- "GSE11675" out.dir <- "~/Downloads/GSE11675" GEOquery::getGEO(GEO = geo.accession, GSEMatrix = T, AnnotG ...
geoquery getgeo written 5 weeks ago by rubi90
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Comment: C: Does fgsea order the stats argument?
... Sorry for the late response. I'm using a Bayesian differential expression tool (MMDIFF), which provides an estimate of the effect size (e.g. ln(fold-change) between treatment and control), the posterior probability that the estimated effect size is different from 0. Unlike the frequentist approaches ...
written 5 weeks ago by rubi90
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Comment: C: Getting error using GenomicRanges::setdiff
... Right, sorry about that and thanks a lot for the help. ...
written 8 months ago by rubi90
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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 8 months ago by rubi90
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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 8 months ago by rubi90 • updated 8 months ago by Martin Morgan ♦♦ 21k
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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 8 months ago by rubi90 • updated 8 months ago by Michael Lawrence10.0k
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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 8 months ago by rubi90 • updated 8 months ago by Michael Lawrence10.0k

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Supporter 14 months ago, voted at least 25 times.

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