User: Robert Ivanek

gravatar for Robert Ivanek
Robert Ivanek350
Reputation:
350
Status:
Trusted
Location:
Switzerland
Last seen:
19 hours ago
Joined:
4 years, 7 months ago
Email:
r************@unibas.ch

Posts by Robert Ivanek

<prev • 51 results • page 1 of 6 • next >
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Answer: A: Normalization of AlignmentsTrack / coverage plot by library size
... Hi, You did not provide any code. It is hard to guess where the problem could be.  Typical mistake is not using full argument name. You need to provide the transformation function as argument called "transformation". The name has to be exact. For example this works for me: library(Gviz) afrom &l ...
written 1 day ago by Robert Ivanek350
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Answer: A: Gviz ChromHMM colouring for AnnotationTracks
... Hi, I can produce a colored plot  annotationTrack above: Tcell_effmem_pblood <- data.frame(seqnames = c("chr3", "chr3", "chr3", "chr3", "chr3"), start = c(3151401L, 3152201L, 3167601L, 3168001L, 3168401L), end = c(3152200L, 3152600L, 3168000L, 3168400L, 3169400L), ...
written 8 days ago by Robert Ivanek350
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Answer: A: Cannot specify groups when overlaying aligned read tracks
... Hi John, You can either use annotation tracks and then code similar to this one should work: T1 <- AnnotationTrack(reads1, feature = factor(rep("sample 1",length(reads1)), levels = c("sample 1", "sample 2")), shape = "box", showId=FALSE) T2 <- AnnotationTrack(reads2, feature = factor(rep("sa ...
written 8 days ago by Robert Ivanek350
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Comment: C: Givz Doesn't plot coverage genetracks that are aligned against ensemble ref
... You need to set ucscChromosomeNames to FALSE. BTW. what is the meaning of "!!!!???" is this a command? options(ucscChromosomeNames=FALSE) ...
written 25 days ago by Robert Ivanek350
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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 25 days ago by Robert Ivanek350
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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 25 days ago by Robert Ivanek350
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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 6 months ago by Robert Ivanek350
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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 8 months ago by Robert Ivanek350
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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 11 months ago by Robert Ivanek350
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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 12 months ago by Robert Ivanek350 • updated 12 months ago by Aaron Lun17k

Latest awards to Robert Ivanek

Scholar 19 months ago, created an answer that has been accepted. For A: gviz: error when plotting BiomartGeneRegionTrack with just.group="above"
Scholar 19 months ago, created an answer that has been accepted. For A: Gviz GeneRegionTrack draw only one gene in the range
Scholar 19 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: error when plotting BiomartGeneRegionTrack with just.group="above"
Scholar 21 months ago, created an answer that has been accepted. For A: gviz: error when plotting BiomartGeneRegionTrack with just.group="above"
Scholar 22 months ago, created an answer that has been accepted. For A: gviz: error when plotting BiomartGeneRegionTrack with just.group="above"
Scholar 2.1 years ago, created an answer that has been accepted. For A: gviz: error when plotting BiomartGeneRegionTrack with just.group="above"
Scholar 2.6 years ago, created an answer that has been accepted. For A: gviz: error when plotting BiomartGeneRegionTrack with just.group="above"

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