User: Robert Ivanek

gravatar for Robert Ivanek
Robert Ivanek530
Reputation:
530
Status:
Trusted
Location:
Switzerland
Last seen:
1 week, 5 days ago
Joined:
5 years, 2 months ago
Email:
r************@unibas.ch

Posts by Robert Ivanek

<prev • 69 results • page 1 of 7 • next >
0
votes
1
answers
46
views
1
answers
Answer: A: gviz: DataTrack: histogram like barplot baseline changed to most negative values
... You can set the y-axis limits. library(Gviz) dt <- DataTrack(GRanges("chr1", IRanges(1:100,1:100), value=sample(-c(20,50), 100, replace=T))) plotTracks(dt, type="histogram", ylim=c(-50,0))   ...
written 17 days ago by Robert Ivanek530
0
votes
3
answers
67
views
3
answers
Answer: A: How to obtain summary statistics for all Bioc releases
... Dear Martin and Peter, Thanks a lot for your helpful answers.  Best, Robert   ...
written 25 days ago by Robert Ivanek530
5
votes
3
answers
67
views
3
answers
How to obtain summary statistics for all Bioc releases
... Dear all, Is there a way to fetch summary statistics (programmatically) of all Bioc releases? * date of release  * number of packages * number of packages in biocViews (optionally) Unfortunately the information is not available on the release page (or not completely) https://bioconductor.org/ab ...
bioconductor release written 25 days ago by Robert Ivanek530
0
votes
1
answers
57
views
1
answers
Answer: A: Gviz: Flip tracks so 5 prime end always on left hand side.
... Hi, I believe you do not need to spend hours with Illustrator but few minutes with vignette :) plotTracks has argument ‘reverseStrand’, by setting it to TRUE will do what you want. Best Robert > On 22 May 2018, at 20:59, stephen.williams [bioc] <noreply@bioconductor.org> wrote: > > ...
written 4 weeks ago by Robert Ivanek530
0
votes
1
answers
77
views
1
answers
Answer: A: Error GC content and conservation visualization with Gviz
... Hi, I believe it is caused by the fact that UCSC does not allow you to fetch large hunks of data (it is also mentioned in the rtracklayer vignette). Either you need to download the files from FTP and read them into Gviz or fetch the data in small chunks and combine afterwards.  Best, Robert ...
written 5 weeks ago by Robert Ivanek530
0
votes
0
answers
95
views
0
answers
Job: Postdoctoral Position: Posttranscriptional gene regulation in T cells (analysis of RNAseq, metabolomics)
... Postdoctoral Position: Posttranscriptional gene regulation in T cells The Molecular Immune Regulation group at the Department of Biomedicine of the University of Basel and Basel University Hospital in Switzerland is seeking a highly motivated postdoc to work at the intersection of immunology, compu ...
rnaseq metabolomics job switzerland basel written 10 weeks ago by Robert Ivanek530
0
votes
1
answers
81
views
1
answers
Answer: A: Gvis: Adding colour and transparency to overlaid alignment tracks
... I believe you can achieve that if you change colouring and alpha level of individual tracks before making an OverlayTrack in Gviz package. There is an example in the Gviz vignette with DataTrack. But the same applies to other track types too. Here is an example using AlignmentTrack class.  library ...
written 3 months ago by Robert Ivanek530
0
votes
0
answers
142
views
0
answers
Comment: C: Gviz: Draw horizontal line on DataTrack
... Did you also looked into Gviz vignette? Please have a look into DataTrack chapter, paragraph "Data Grouping". Is that you are looking for? Best Robert   ...
written 3 months ago by Robert Ivanek530
0
votes
1
answers
121
views
1
answers
Answer: A: Can GViz show multiple HighlightTrack with multiple colors in the same track?
... Dear Ignacio, If I understood you correctly, you want to use different colours for highlighted region in  HighlightTrack object. But that works already now.  Let me know if that is sufficient for you. Best, Robert   library(Gviz) data(cpgIslands) chr <- as.character(unique(seqnames(cpgIslan ...
written 3 months ago by Robert Ivanek530
0
votes
1
answers
221
views
1
answers
Comment: C: gviz ideogramTrack connection error
... BTW. What is your sessionInfo?   ...
written 4 months ago by Robert Ivanek530

Latest awards to Robert Ivanek

Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Gvis: Adding colour and transparency to overlaid alignment tracks
Scholar 14 months ago, created an answer that has been accepted. For A: gviz: error when plotting BiomartGeneRegionTrack with just.group="above"
Scholar 14 months ago, created an answer that has been accepted. For A: Gviz GeneRegionTrack draw only one gene in the range
Scholar 14 months ago, created an answer that has been accepted. For A: Different junction numbers from sashimi plot of Gviz package and summarizeJuncti
Scholar 14 months ago, created an answer that has been accepted. For A: Gviz: AlignmentsTrack from a bam file with non-UCSC chromosome names
Scholar 2.2 years ago, created an answer that has been accepted. For A: Gviz GeneRegionTrack draw only one gene in the range
Scholar 2.2 years ago, created an answer that has been accepted. For A: gviz: error when plotting BiomartGeneRegionTrack with just.group="above"
Scholar 2.2 years ago, created an answer that has been accepted. For A: gviz: error when plotting BiomartGeneRegionTrack with just.group="above"
Scholar 2.4 years ago, created an answer that has been accepted. For A: gviz: error when plotting BiomartGeneRegionTrack with just.group="above"
Scholar 2.4 years ago, created an answer that has been accepted. For A: gviz: error when plotting BiomartGeneRegionTrack with just.group="above"
Scholar 2.5 years ago, created an answer that has been accepted. For A: gviz: error when plotting BiomartGeneRegionTrack with just.group="above"
Scholar 2.7 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"

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 143 users visited in the last hour