Moderator: Michael Lawrence

gravatar for Michael Lawrence
Michael Lawrence10.0k
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Joined:
8 years, 4 months ago
Email:
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Posts by Michael Lawrence

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Answer: A: S4Vectors and subectHits error
... It would help to see your sessionInfo() output. My guess is that you are using a years old version that still expects to be getting the subjectHits symbol from IRanges. ...
written 7 days ago by Michael Lawrence10.0k
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Answer: A: rtracklayer::liftOver parameters (minMatch)
... I could look into it, but no promises. The rtracklayer liftOver is a complete reimplementation of the UCSC liftover tool, which is only freely available for academic use. I've avoided even looking at the liftover source code. ...
written 14 days ago by Michael Lawrence10.0k
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Comment: C: Detect Sites with Minimum Gap in GRanges Object
... It would help to know more about your high-level use case. Why are you doing this? ...
written 15 days ago by Michael Lawrence10.0k
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Answer: A: rtracklayer colorByStrand - is it possible to add quotes?
... Thanks, should be fixed in devel, 1.39.10. Btw, potential bugs are often better reported as a GitHub issue. ...
written 15 days ago by Michael Lawrence10.0k
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Answer: A: Detecting Overlaps within Grange Object
... So you don't consider them overlapping if they overlap by 1 position? Or do you want end(b) >= start(a) & end(a) >= start(b)? Either way, that can be controlled via arguments to findOverlaps(). When passing a single ranges object to findOverlaps(), it will find overlaps within the set of r ...
written 27 days ago by Michael Lawrence10.0k
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Answer: A: Features within 2kb window, but with resampling
... Probably want something like: bins <- reduce(x, min.gapwidth=2000L) If you want to know which ranges fell into each bin, use , with.revmap=TRUE. ...
written 4 weeks ago by Michael Lawrence10.0k
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Answer: A: import bed file with track line fails
... I don't think this has to do with the trackline. It's just that your file is not tab-separated, which is required by the BED spec. UCSC might be more forgiving, but we recently moved to require tab separation, because not abiding by the spec was causing problems. Also, btw, extraCols needs to be na ...
written 4 weeks ago by Michael Lawrence10.0k
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Answer: A: rtracklayer demo bug
... I pushed a fix for this to the release and devel branches. It's an ancient demo, so it has code rotted a bit and has been broken like this for 2 years. ...
written 5 weeks ago by Michael Lawrence10.0k
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Answer: A: Finding the nearest n genes from a genomic loci
... There is a hidden function GenomicRanges:::findKNN() that might do the trick. It's largely untested so let me know whether it works. ...
written 5 weeks ago by Michael Lawrence10.0k
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Comment: C: Splitting lines of a GRanges object based on character list
... Depending on the context, of course. ...
written 6 weeks ago by Michael Lawrence10.0k

Latest awards to Michael Lawrence

Scholar 10 months ago, created an answer that has been accepted. For A: trying to annotate overlaps with external file information
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: trying to annotate overlaps with external file information
Scholar 11 months ago, created an answer that has been accepted. For A: trying to annotate overlaps with external file information
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: trying to annotate overlaps with external file information
Scholar 11 months ago, created an answer that has been accepted. For A: trying to annotate overlaps with external file information
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: trying to annotate overlaps with external file information
Scholar 11 months ago, created an answer that has been accepted. For A: trying to annotate overlaps with external file information
Scholar 11 months ago, created an answer that has been accepted. For A: filtering VCF files
Scholar 12 months ago, created an answer that has been accepted. For A: Genomic Ranges findOverlaps by sample
Scholar 12 months ago, created an answer that has been accepted. For A: filtering VCF files
Scholar 12 months ago, created an answer that has been accepted. For A: filtering VCF files
Scholar 13 months ago, created an answer that has been accepted. For A: filtering VCF files
Scholar 13 months ago, created an answer that has been accepted. For A: filtering VCF files
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: filtering VCF files
Scholar 13 months ago, created an answer that has been accepted. For A: Genomic Ranges findOverlaps by sample
Scholar 13 months ago, created an answer that has been accepted. For A: Genomic Ranges findOverlaps by sample
Scholar 14 months ago, created an answer that has been accepted. For A: Genomic Ranges findOverlaps by sample
Scholar 14 months ago, created an answer that has been accepted. For A: Genomic Ranges findOverlaps by sample
Scholar 14 months ago, created an answer that has been accepted. For A: setdiff for GenomicRanges
Scholar 14 months ago, created an answer that has been accepted. For A: Genomic Ranges findOverlaps by sample
Scholar 14 months ago, created an answer that has been accepted. For A: Genomic Ranges findOverlaps by sample
Teacher 24 months ago, created an answer with at least 3 up-votes. For A: setdiff for GenomicRanges
Teacher 24 months ago, created an answer with at least 3 up-votes. For A: Operations across Lists of GenomicRanges?
Scholar 24 months ago, created an answer that has been accepted. For A: setdiff between GenomicRanges objects keeping metadata
Scholar 24 months ago, created an answer that has been accepted. For A: Operations across Lists of GenomicRanges?

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