Moderator: Michael Lawrence

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Michael Lawrence10.0k
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Posts by Michael Lawrence

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Comment: C: Merging each element of a list of Genomic range
... I assumed by "gene" the OP meant "transcript". To do it by gene, you would need to use the gene IDs instead. Trans-splicing is another complication though, where there will be multiple ranges per transcript, on different sequences and/or strands. But it's easy to restrict to length one elements befo ...
written 11 days ago by Michael Lawrence10.0k
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Answer: A: Merging each element of a list of Genomic range
... It's not exactly clear what you want. If you want a GRanges of the total span of the CDS blocks for each gene, you could do: unlist(range(cds_grl)) ...
written 11 days ago by Michael Lawrence10.0k
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Comment: C: unlist doesn't work for IRanges
... For now I guess you'll just have to use IRanges:::unlist_as_integer(). I'm hoping that there is a way to achieve the same effect in the future using an exported entry point. ...
written 26 days ago by Michael Lawrence10.0k
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Comment: C: rtracklayer::lifOver one-to-many regions and not match UCSC
... Consistency with the UCSC liftOver is going to be tough, since the algorithm is not well described and the code has a restricted license. It looks like it does some smoothing and filtering on top of the chain mappings. Exactly how would take a lot of reverse engineering. ...
written 26 days ago by Michael Lawrence10.0k
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Comment: C: Issue with UCSC and rtracklayer: 'names' attribute [210] must be the same length
... The basic problem is that rtracklayer was originally designed as an interface to the genome browser, not the database. It interacts with the web site directly, relying on a myriad of heuristics. People have come to use it almost exclusively as an interface to the database, so really it should just b ...
written 6 weeks ago by Michael Lawrence10.0k
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Answer: A: Issue with UCSC and rtracklayer: 'names' attribute [210] must be the same length
... This has been fixed in devel and release (1.40.1) thanks to Jim McDonald. I put in a more robust (hopefully) heuristic in 1.40.2. ...
written 6 weeks ago by Michael Lawrence10.0k
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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 9 weeks 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 10 weeks 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 10 weeks 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 10 weeks ago by Michael Lawrence10.0k

Latest awards to Michael Lawrence

Scholar 12 months ago, created an answer that has been accepted. For A: setdiff for GenomicRanges
Scholar 12 months ago, created an answer that has been accepted. For A: Features within 2kb window, but with resampling
Scholar 12 months ago, created an answer that has been accepted. For A: What is the proper way to modify mcols of a GRanges inside a GRangesList?
Scholar 12 months ago, created an answer that has been accepted. For A: reduce function after combining 2 GRanges objects from cn.mops output
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: Subset GRanges object into new object
Scholar 12 months ago, created an answer that has been accepted. For A: VariantAnnotation - expand not working as intended for VCF
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: trying to annotate overlaps with external file information
Scholar 12 months ago, created an answer that has been accepted. For A: closest-features equivalent in Bioconductor for finding closest gene(s)
Scholar 12 months ago, created an answer that has been accepted. For A: unlist a exons GRangeslist object and add a gene name column
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: Can rtracklayer import tab-delimited BED files with unquoted spaces in fields?
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: unlist a exons GRangeslist object and add a gene name column
Scholar 12 months ago, created an answer that has been accepted. For A: trying to annotate overlaps with external file information
Scholar 12 months ago, created an answer that has been accepted. For A: Why export of empty GRanges to GFF fails?
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: annotate GRanges with upstream or downstream nearest gene
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: filtering VCF files
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: setdiff for GenomicRanges
Scholar 12 months ago, created an answer that has been accepted. For A: issue renaming seqnames in genomic ranges
Scholar 12 months ago, created an answer that has been accepted. For A: does import.bw with the selection argument take into account strand?
Scholar 12 months ago, created an answer that has been accepted. For A: VariantAnnotation as.vranges with asterisk in ALT field
Scholar 12 months ago, created an answer that has been accepted. For A: Group GRanges and keep metadata
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: What is the proper way to modify mcols of a GRanges inside a GRangesList?
Popular Question 12 months ago, created a question with more than 1,000 views. For Job Opening: Computational Biologist @ Genentech Bioinformatics
Scholar 12 months ago, created an answer that has been accepted. For A: Detecting Overlaps within Grange Object

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