User: Robert Ivanek

gravatar for Robert Ivanek
Robert Ivanek590
Reputation:
590
Status:
Trusted
Location:
Switzerland
Last seen:
1 week, 5 days ago
Joined:
6 years ago
Email:
r************@unibas.ch

Posts by Robert Ivanek

<prev • 85 results • page 1 of 9 • next >
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Comment: C: Gviz: decreasing tick resolution
... Hi Will, It works for me. Can you post your code? Best, Robert ...
written 23 days ago by Robert Ivanek590
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Job: Postdoctoral Fellow in Genomics (University of Basel, Switzerland)
... __Postdoctoral Position: Bioinformatics (100%)__ The [Molecular Immune Regulation group](https://biomedizin.unibas.ch/en/research/research-groups/jeker-lab/) at the Department of Biomedicine of the University Hospital Basel in Switzerland is seeking a highly motivated postdoc with a strong backgrou ...
job postdoc switzerland basel written 28 days ago by Robert Ivanek590
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Comment: C: Adding a legend to a GeneRegionTrack?
... Hi, Currently it is implemented only for `DataTrack-Class`. Do you have an example code where do you want to use it? Best, Robert ...
written 6 weeks ago by Robert Ivanek590
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Answer: A: Truncated Gviz plot
... Hi Mario, Thanks for reporting it. I changed settings for "sashimi" plots in Gviz. There should be new version compiled in release (1.26.5) and in development (1.27.6). They should be available in next few days. Let me know if that fixed your problem. Best Robert ...
written 8 weeks ago by Robert Ivanek590
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Comment: C: Error loading Gviz package object path is not exported by namespace:Rsamtools
... Hi, what is the version of `Gviz` package you are using? Best Robert ...
written 3 months ago by Robert Ivanek590
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Comment: C: Gviz: decreasing tick resolution
... You need to specify the positions of tick marks, i.e. seq(280e3, 320e3, 40e3). Complete example: library(Gviz) axisTrack <- GenomeAxisTrack() plotTracks(axisTrack, from=270e3, to=330e3) with ticksAt parameter: plotTracks(axisTrack, from=270e3, to=330e3, ticksAt=seq(280e3, 320e3, 40e3)) ...
written 3 months ago by Robert Ivanek590
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Answer: A: Gviz color alignments by read strand
... The way how Gviz handles colouring for AlignmentsTrack is a bit special. It recycles colours specified in the fill.reads along the length of unique read ids (uid column). On top of it, if you plot reads as arrows, it also sorts the reads before plotting according to the strand. Maybe this piece of ...
written 3 months ago by Robert Ivanek590
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Comment: C: Gviz color alignments by read strand
... Hi Chris, what exactly do you want to achieve? Do you want to plot individual reads (coloured by the read strand) or coverage (histogram) for both strands separately? Robert ...
written 3 months ago by Robert Ivanek590
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Comment: C: Gviz: decreasing tick resolution
... Yes, that is correct. I think that installing devel version of R and all the packages might be an overkill, especially for one figure. If you do not mind to use a dirty hack you can also install the devel version of Gviz in current release version of R (assuming all dependencies for release version ...
written 3 months ago by Robert Ivanek590
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Answer: A: Gviz: decreasing tick resolution
... Hi Will, I added new parameter called ticksAt for GenomeAxisTrack. It will be available in developmental version of Gviz (1.27.5) (Bioc 3.9) Best Robert ...
written 3 months ago by Robert Ivanek590

Latest awards to Robert Ivanek

Scholar 3 months ago, created an answer that has been accepted. For A: Gviz GeneRegionTrack draw only one gene in the range
Scholar 3 months ago, created an answer that has been accepted. For A: gviz: error when plotting BiomartGeneRegionTrack with just.group="above"
Scholar 24 months ago, created an answer that has been accepted. For A: Gviz: AlignmentsTrack from a bam file with non-UCSC chromosome names
Scholar 24 months ago, created an answer that has been accepted. For A: Gviz GeneRegionTrack draw only one gene in the range
Scholar 24 months ago, created an answer that has been accepted. For A: Different junction numbers from sashimi plot of Gviz package and summarizeJuncti
Scholar 24 months ago, created an answer that has been accepted. For A: gviz: error when plotting BiomartGeneRegionTrack with just.group="above"
Teacher 24 months ago, created an answer with at least 3 up-votes. For A: Gvis: Adding colour and transparency to overlaid alignment tracks
Scholar 3.0 years ago, created an answer that has been accepted. For A: gviz: error when plotting BiomartGeneRegionTrack with just.group="above"
Scholar 3.0 years ago, created an answer that has been accepted. For A: Gviz GeneRegionTrack draw only one gene in the range
Scholar 3.1 years ago, created an answer that has been accepted. For A: gviz: error when plotting BiomartGeneRegionTrack with just.group="above"
Scholar 3.2 years ago, created an answer that has been accepted. For A: gviz: error when plotting BiomartGeneRegionTrack with just.group="above"
Scholar 3.2 years ago, created an answer that has been accepted. For A: gviz: error when plotting BiomartGeneRegionTrack with just.group="above"
Scholar 3.3 years ago, created an answer that has been accepted. For A: gviz: error when plotting BiomartGeneRegionTrack with just.group="above"
Scholar 3.6 years ago, created an answer that has been accepted. For A: gviz: error when plotting BiomartGeneRegionTrack with just.group="above"
Scholar 4.0 years ago, created an answer that has been accepted. For A: gviz: error when plotting BiomartGeneRegionTrack with just.group="above"

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