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 • 220 results • page 1 of 22 • next >
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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 13 hours ago by florian.hahne@novartis.com1.5k
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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 10 days ago by florian.hahne@novartis.com1.5k
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Answer: A: A bug when plotting Gviz data
... Hi Dadi, could you compile a short reproducible example for me to take a look at? Also pointing out what exactly gets messed up? Thanks, Florian ...
written 5 weeks ago by florian.hahne@novartis.com1.5k
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Answer: A: Gviz : sort reads in AlignmentsTracks and display reads containing indels
... You can't really sort reads in these visualisations. Gviz tries to arrange the reads in a way to minimize the vertical space that is needed for display. Also, indels are currently not supported. I am happy to add functionality to the package if somebody else in the developer realm want's to take a f ...
written 4 months ago by florian.hahne@novartis.com1.5k
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Comment: C: Regarding Gviz package
... I'd recommend for you to read up a bit on how to import Excel or tab delimited files into R, and also on the way Bioconductor handles genomic ranges. Gviz is very flexible in terms of inputs. You can provide a data.frame, a GRanges object, paths to various file formats or even populate the necessary ...
written 5 months ago by florian.hahne@novartis.com1.5k
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Answer: A: Gviz transcriptAnnotation with gff
... GeneRegionTrack objects are not simple wrappers around GRanges objects, but instead impose a certain structure like gene identifiers, transcript identifiers and human readable gene symbols. Thus it expects the input data to populate these required properties. Your repeat masker data is not really ge ...
written 6 months ago by florian.hahne@novartis.com1.5k
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Answer: A: Gviz AnnotationTrack id above feature
... How about this: plotTracks(list(cpgTrack), legend = TRUE, groupAnnotation="id", just.group = "above") ...
written 6 months ago by florian.hahne@novartis.com1.5k
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Answer: A: Gviz off-by-one with STAR BAM
... Hi Bernt, looks like a 0 vs 1 offset issue. I am a bit surprised that this did not occur earlier. Have to check whether something changed in the core tools that we are using for reading the BAM files. Is there a chance that you could upload the section from bamfile1 shown in you example to that dro ...
written 7 months ago by florian.hahne@novartis.com1.5k
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Answer: A: Error using Gviz and BiomartGeneRegionTrack, version problem?
... Well, this is a bit problematic if you are dealing with dynamic data sources like Biomart and UCSC. You can always transform a BiomartGeneRegionTrack into a regular GeneRegionTrack by calling as(biomTrack, "GeneRegionTrack") and at that stage you can manipulate the GRanges object inside the track ...
written 7 months ago by florian.hahne@novartis.com1.5k
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Comment: C: Error using Gviz and BiomartGeneRegionTrack, version problem?
... Once Gviz version 1.18.2 becomes available you can go directly with the default biomart solution: options(ucscChromosomeNames=FALSE) biomTrack <- BiomartGeneRegionTrack(genome = "gasacu1",chromosome = "groupI", start = 20000000, end = 21000000,name = "ENSEMBL") Please note that ESEMBL uses "gr ...
written 7 months ago by florian.hahne@novartis.com1.5k

Latest awards to florian.hahne@novartis.com

Popular Question 5 months ago, created a question with more than 1,000 views. For displaying coverage RNAseq Gviz
Scholar 6 months ago, created an answer that has been accepted. For A: Create custom IdeogramTrack (Gviz)
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Create custom IdeogramTrack (Gviz)
Scholar 7 months ago, created an answer that has been accepted. For A: Create custom IdeogramTrack (Gviz)
Scholar 8 months ago, created an answer that has been accepted. For A: Create custom IdeogramTrack (Gviz)
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Create custom IdeogramTrack (Gviz)
Scholar 8 months ago, created an answer that has been accepted. For A: Create custom IdeogramTrack (Gviz)
Scholar 18 months ago, created an answer that has been accepted. For A: Gviz: HighlightTrack on AlignmentsTrack - over pileup (reads) but behind coverag
Scholar 18 months ago, created an answer that has been accepted. For A: Create custom IdeogramTrack (Gviz)
Scholar 18 months ago, created an answer that has been accepted. For A: Gviz Color Filling
Scholar 18 months ago, created an answer that has been accepted. For A: Gviz: Set height to avoid empty whitespace below reads in an AlignmentsTrack?
Scholar 18 months ago, created an answer that has been accepted. For A: Gviz Color Filling
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: Create custom IdeogramTrack (Gviz)
Scholar 18 months ago, created an answer that has been accepted. For A: Gviz: HighlightTrack on AlignmentsTrack - over pileup (reads) but behind coverag
Scholar 19 months ago, created an answer that has been accepted. For A: Gviz: How to color parts of transcript in BiomartGeneRegionTrack?
Scholar 19 months ago, created an answer that has been accepted. For A: Gviz: How to color parts of transcript in BiomartGeneRegionTrack?
Scholar 19 months ago, created an answer that has been accepted. For A: Gviz: Keep transcripts on same line even when using reverseStrand+showId?
Scholar 20 months ago, created an answer that has been accepted. For A: Gviz: How to color parts of transcript in BiomartGeneRegionTrack?
Scholar 20 months ago, created an answer that has been accepted. For A: Gviz: How to color parts of transcript in BiomartGeneRegionTrack?
Scholar 20 months ago, created an answer that has been accepted. For A: Gviz: HighlightTrack doesn't react to reverseStrand = TRUE ?
Scholar 20 months ago, created an answer that has been accepted. For A: Gviz: Keep transcripts on same line even when using reverseStrand+showId?
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: Gviz - show plus and minus strand from a bam
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: Gviz highlighted regions displaying behind main plot
Centurion 2.5 years ago, created 100 posts.
Scholar 2.7 years ago, created an answer that has been accepted. For A: Gviz highlighted regions displaying behind main plot

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