User: florian.hahne@novartis.com

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Before joining biomedical research in big pharma here at Novartis I have been a member of the Bioconductor core team in Seattle. My scientific interests are the analysis of genomics and genetics data in all colours and flavour, data visualisation and software engineering as well as integration and mining of various types of toxicology-related data.

I am the maintainer and co-author of a number of packages, including Gviz for visualization of data along genomic coordinates, cellHTS2 for the analysis of high-throughput cell-based assays, and some of the flow cytometry infrastructure packages.

Posts by florian.hahne@novartis.com

<prev • 228 results • page 1 of 23 • next >
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Comment: C: Gviz: ylim of the AlignmentsTrack
... Gviz applies a bit of smoothing in order to make the coverage plot look a bit more appealing: res <- .pxResolution(coord = "x") brks <- ceiling((maxBase - mminBase)/res) x <- seq(mminBase, maxBase, len = brks) y <- tapply(as.integer(cov[mminBase:maxBase]), cut(mminBase:maxBase, breaks ...
written 7 weeks ago by florian.hahne@novartis.com1.6k
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Answer: A: Gviz: ylim of the AlignmentsTrack
... I am not quite sure I understand. Unless provided explicitly, the ylim values should already be computed dynamically. If that is not the desired range, you will need to compute coverage at the region to be plotted from you bam file manually and explicitly set ylim with the max coverage value. There ...
written 7 weeks ago by florian.hahne@novartis.com1.6k
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Comment: C: Gviz Alignment Tracks with non-UCSC reference chromosome names
... Could you create a small reproducible example, maybe with a stripped down version of the BAM file? Regardless of the chromosome issue, this should fail more gracefully. Could you please try and set  options(ucscChromosomeNames=FALSE) That might help with the non-standard chromosome identifiers. ...
written 8 weeks ago by florian.hahne@novartis.com1.6k
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Answer: A: Gviz change color of groups
... Have you tried the obvious? dat <- matrix(runif(400), nrow=4) dtTrack <- DataTrack(start=seq(1,1000, len=100), width=10, data=dat, chromosome=1, genome="mm9", name="random data") library(GenomicRanges) gr <- GRanges(seqnames="chr1", ranges=IRanges(seq(1,1000, len=100), width=10)) valu ...
written 3 months ago by florian.hahne@novartis.com1.6k
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Comment: C: GVIZ - Manually assign transcript to stacks?
...   Did you try collapse=FALSE in the BiomartGeneRegionTrack constructor? Individual transcripts should never get collapsed, but just to make sure. There is no real control over the stacking as this tries to optimize for the available space, but you can do some tricks. For instance, including a tran ...
written 5 months ago by florian.hahne@novartis.com1.6k
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Comment: C: gviz ideogramTrack connection error
... In 99% of cases, this is an issue with the rtracklayer connection to UCSC. Gviz does not implement any of that functionality. I'd advise to test whether the rtracklayer UCSC functionality works for you, and if not, to reach out to the rtracklayer package maintainers. Florian ...
written 9 months ago by florian.hahne@novartis.com1.6k
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Answer: A: Gviz: Help figuring out `arguments imply differing number of rows: 0, 1` error
... Looks a lot like a bug to me.  data.frame(x1 = start(pairGaps) - 1, y1 = gy, x2 = end(pairGaps) + 1, y2 = gy, col = .dpOrDefault(GdObject, c("col.mates", "col"), .DEFAULT_BRIGHT_SHADED_COL), lwd = .dpOrDefault(GdObject, c("lwd.mates", "lwd"), 1), lty = .dpOrDefault(GdObject ...
written 11 months ago by florian.hahne@novartis.com1.6k
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Comment: C: Givz Doesn't plot coverage genetracks that are aligned against ensemble ref
... Obviously you will need to use the numerical chromosome name now also for plotting: plotTracks(list(idxTrack, axTrack, ensGenes ,mutant, wildtype),from=from, to=to, showTitle=T, showId=T, fontsize = 18, chromosome = 8) IGV is irrelevant, you are not changing your BAM file here. If you need more ...
written 12 months ago by florian.hahne@novartis.com1.6k
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Answer: A: Givz Doesn't plot coverage genetracks that are aligned against ensemble ref
... Are you sure that the chromosome names match? Sometimes you will only have the numeric part (e.g., 8) in your BAM file. A bit hard to say what is going wrong without seeing the actual data. Also, have you considered using the somewhat more specialised AlignmentsTrack class? It will be way more effi ...
written 12 months ago by florian.hahne@novartis.com1.6k
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Comment: C: R Gviz ideogram custom track
... I don't think that the initial band definitions make any sense. Why would you define bands that all start at the same location? Gviz doesn't really check the consistency of the band definition, but rather naively tries to draw polygons. I assume that is what you are seeing. Try defining non-overlapp ...
written 13 months ago by florian.hahne@novartis.com1.6k

Latest awards to florian.hahne@novartis.com

Popular Question 9 months ago, created a question with more than 1,000 views. For Gviz question
Scholar 9 months ago, created an answer that has been accepted. For A: Create custom IdeogramTrack (Gviz)
Popular Question 17 months ago, created a question with more than 1,000 views. For Gviz question
Popular Question 17 months ago, created a question with more than 1,000 views. For displaying coverage RNAseq Gviz
Popular Question 17 months ago, created a question with more than 1,000 views. For Gviz problem to extract some track with UcscTrack like Broad ChromHMM
Popular Question 18 months ago, created a question with more than 1,000 views. For displaying coverage RNAseq Gviz
Scholar 19 months ago, created an answer that has been accepted. For A: Create custom IdeogramTrack (Gviz)
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: Create custom IdeogramTrack (Gviz)
Scholar 20 months ago, created an answer that has been accepted. For A: Create custom IdeogramTrack (Gviz)
Scholar 21 months ago, created an answer that has been accepted. For A: Create custom IdeogramTrack (Gviz)
Scholar 21 months ago, created an answer that has been accepted. For A: Create custom IdeogramTrack (Gviz)
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: Create custom IdeogramTrack (Gviz)
Scholar 2.6 years ago, created an answer that has been accepted. For A: Gviz: HighlightTrack on AlignmentsTrack - over pileup (reads) but behind coverag
Teacher 2.6 years ago, created an answer with at least 3 up-votes. For A: Create custom IdeogramTrack (Gviz)
Scholar 2.6 years ago, created an answer that has been accepted. For A: Gviz Color Filling
Scholar 2.6 years ago, created an answer that has been accepted. For A: Gviz: Set height to avoid empty whitespace below reads in an AlignmentsTrack?
Scholar 2.6 years ago, created an answer that has been accepted. For A: Gviz Color Filling
Scholar 2.6 years ago, created an answer that has been accepted. For A: Create custom IdeogramTrack (Gviz)
Scholar 2.6 years ago, created an answer that has been accepted. For A: Gviz: HighlightTrack on AlignmentsTrack - over pileup (reads) but behind coverag
Scholar 2.6 years ago, created an answer that has been accepted. For A: Gviz: How to color parts of transcript in BiomartGeneRegionTrack?
Scholar 2.6 years ago, created an answer that has been accepted. For A: Gviz: Keep transcripts on same line even when using reverseStrand+showId?
Scholar 2.6 years ago, created an answer that has been accepted. For A: Gviz: How to color parts of transcript in BiomartGeneRegionTrack?
Scholar 2.7 years ago, created an answer that has been accepted. For A: Gviz: How to color parts of transcript in BiomartGeneRegionTrack?
Scholar 2.7 years ago, created an answer that has been accepted. For A: Gviz: How to color parts of transcript in BiomartGeneRegionTrack?
Scholar 2.7 years ago, created an answer that has been accepted. For A: Gviz: Keep transcripts on same line even when using reverseStrand+showId?

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