User: theodore.georgomanolis

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Posts by theodore.georgomanolis

<prev • 32 results • page 1 of 4 • next >
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diffbind dba.plotvolcano bLabels option use genames instead of numbers
... Hi all, So am using the diffbind R package and I was doing some plots after analyzing my samples. using the dba.plotVolcano and the option > bLabels = TRUE I can have the location of those 50 genes that are on the top of the list. That is great but is not that informative Is it possible inst ...
diffbind written 12 hours ago by theodore.georgomanolis0
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error in readPeakFile {chipseeker}
... Hi all, So I got several bed files as created by MACS2. I am loading them as list with the following: peaks <- as.list(c("K002000291_97925.narrowPeak", "K002000291_97926.narrowPeak", "K002000291_97927.narrowPeak", ...
chipseeker readpeakfile written 6 weeks ago by theodore.georgomanolis0
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Comment: C: Problem in using covplot ChIPseeker
... same here, got the same problem ...
written 6 weeks ago by theodore.georgomanolis0
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Comment: C: atacseqQC error while splittin the bamfile
... by the way the script I used was the one provided I changed nothing in order to see if it works in my case. Session info: > `> sessionInfo()` > R version 3.6.0 (2019-04-26) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Linux Mint 18.3 > > Matrix products: default BLAS: /us ...
written 6 weeks ago by theodore.georgomanolis0
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Comment: C: atacseqQC error while splittin the bamfile
... sorry for replying after so long I am sending you an email with the bam file ...
written 6 weeks ago by theodore.georgomanolis0
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atacseqQC error while splittin the bamfile
... Hi all, anyone can help with the following from the ATACseqQC package: objs <- splitBam(bamfile, tags=tags, outPath=outPath, + txs=txs, genome=genome, + conservation=phastCons100way.UCSC.hg19) ERROR as follows: > [E::sam_parse1] unrecognized type ...
error atac-seq atacseqqc split bam file written 7 weeks ago by theodore.georgomanolis0 • updated 6 weeks ago by contact0
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Is it possible to use Rnbeads with WGBS data from epigenetics roadmap/ucsc data
... Dear all, I have a three files from epigenetics roadmap that have already been analyzed and I got the bigwig files with the already calculated percentage of the methylation. Is it possible to use those files perform differential analysis of the methylated sites using Rnbeads? If so, is it possible ...
rnbeads wgbs written 21 months ago by theodore.georgomanolis0
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Comment: C: FourCseq: getZScores errors, first case 6 digenerated cutterm second case 4 base
... Should I send a new question with a DESeq2 tag? ...
written 2.9 years ago by theodore.georgomanolis0
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Comment: C: FourCseq, rawRanges Description
... Hi Felix, I will look at them and come back to you. Thank you again for your help ...
written 2.9 years ago by theodore.georgomanolis0
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FourCseq, rawRanges Description
... Hi Felix once more, I am trying to figure out a few things on the R script and I wandering what the rawRanges holds. I can extract the following items: leftSize rightSize leftValid rightValid mid dist posLeft posRight blind vpChr tooClose lowCounts selectedForF ...
fourcseq written 2.9 years ago by theodore.georgomanolis0 • updated 2.9 years ago by felix.klein150

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Popular Question 2.4 years ago, created a question with more than 1,000 views. For FourCseq - error countFragmentOverlaps()

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