User: Robert Ivanek

gravatar for Robert Ivanek
Robert Ivanek430
Reputation:
430
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Trusted
Location:
Switzerland
Last seen:
1 week ago
Joined:
4 years, 9 months ago
Email:
r************@unibas.ch

Posts by Robert Ivanek

<prev • 57 results • page 2 of 6 • next >
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Comment: C: Givz Doesn't plot coverage genetracks that are aligned against ensemble ref
... Have you also switched off UCSC chromosome naming convention? options(ucscChromosomeNames=FALSE) Otherwise it is for me hard to help without seeing the data and complete code. Can you share it? ...
written 12 weeks ago by Robert Ivanek430
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Comment: C: Givz Doesn't plot coverage genetracks that are aligned against ensemble ref
... You can either use gene model based on ensembl or simply replace the seqlevels in your  ensGenes. seqlevels(ranges(ensGenes)) <- sub("^chr", "", seqlevels(ranges(ensGenes)))   ...
written 12 weeks ago by Robert Ivanek430
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Comment: C: Gviz sashimi read count
... To get those numbers via Gviz seems to me too complicated. You can use package GenomicAlignments to get those numbers from BAM files directly: function readGAlignments or readGAlignmentPairs to read in the data from BAM file and summarizeJunctions to produce the counts for junctions. ...
written 8 months ago by Robert Ivanek430
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Answer: A: Gviz sashimi read count
... Hi Bernt, You can set the parameter sashimiNumbers  to TRUE. Then it should work. Either  when you create the track or when using plotTracks function. Best Robert   ...
written 10 months ago by Robert Ivanek430
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Answer: A: Understanding the height in sashimi plots made by Gviz
... Hi Leo, It is correct, I added the information into vignette. Sorry for not putting it there before. Best Robert ...
written 14 months ago by Robert Ivanek430
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edgeR estimateGLMRobustDisp fails with and error
... Hi, I wanted to estimate the dispersions for RNAseq dataset using the robust version in edgeR package. After running following line of code I got an error in recent version of edgeR/Bioconductor despite the fact that identical code work on the same dataset in previous version of edgeR/Bioconductor: ...
rnaseq edger written 14 months ago by Robert Ivanek430 • updated 14 months ago by Aaron Lun18k
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Answer: A: Gviz Sashimi Plot height/colour/count
... Hi Stefan, I am sorry for the delay. 1) Currently it is possible to adjust the height of "coverage" (or "sashimi") track only if also "pileup" is displayed. Otherwise each of them occupies half of the track height. 2) There was typo in the code. Thank you for pointing it out. "col.sashimi" should ...
written 16 months ago by Robert Ivanek430
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Job: PostDoc Position in Computational Biology of Gene Regulatory Networks and Epigenetics, University of Basel, Switzerland
... Postdoctoral Position in Computational Biology of Gene Regulatory Networks and Epigenetics 100% (available immediately, up to 5 years) This position is part of a 5-year ERC funded research project aiming to get fundamental insights into how signalling inputs orchestrate changes in chromatin and tr ...
job bioinformatician job postdoc switzerland written 17 months ago by Robert Ivanek430
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Job: Bioinformatician 80-100%, Core Facility at the DBM, University of Basel, Switzerland
... Bioinformatician 80-100% The Department of Biomedicine (DBM) at the University of Basel and University Hospital Basel is seeking a Ph.D. level bioinformatician to join the Bioinformatics Core Facility. The position is initially limited to two years with a possibility for permanent extension. The Bi ...
job bioinformatician job core facility written 18 months ago by Robert Ivanek430
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Comment: C: Gviz AlignmentTrack problem
... I believe this might do the trick: levels(itrack@bandTable$chrom) <- sub("^chr", "", levels(itrack@bandTable$chrom)) ...
written 20 months ago by Robert Ivanek430

Latest awards to Robert Ivanek

Scholar 21 months ago, created an answer that has been accepted. For A: gviz: error when plotting BiomartGeneRegionTrack with just.group="above"
Scholar 21 months ago, created an answer that has been accepted. For A: Gviz GeneRegionTrack draw only one gene in the range
Scholar 22 months ago, created an answer that has been accepted. For A: gviz: error when plotting BiomartGeneRegionTrack with just.group="above"
Scholar 23 months ago, created an answer that has been accepted. For A: gviz: error when plotting BiomartGeneRegionTrack with just.group="above"
Scholar 23 months ago, created an answer that has been accepted. For A: gviz: error when plotting BiomartGeneRegionTrack with just.group="above"
Scholar 2.0 years ago, created an answer that has been accepted. For A: gviz: error when plotting BiomartGeneRegionTrack with just.group="above"
Scholar 2.3 years ago, created an answer that has been accepted. For A: gviz: error when plotting BiomartGeneRegionTrack with just.group="above"
Scholar 2.8 years ago, created an answer that has been accepted. For A: gviz: error when plotting BiomartGeneRegionTrack with just.group="above"

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