Moderator: Michael Lawrence

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Michael Lawrence10.0k
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Posts by Michael Lawrence

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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 11 weeks 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 12 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 3 months 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 3 months 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 3 months 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 3 months ago by Michael Lawrence10.0k
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Comment: C: Splitting lines of a GRanges object based on character list
... Why are you coercing to a data frame first? ...
written 3 months ago by Michael Lawrence10.0k
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Answer: A: Splitting lines of a GRanges object based on character list
... expand(grange_test, "SYMBOL") ...
written 3 months ago by Michael Lawrence10.0k
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Comment: C: intronsByTranscript and fiveUTRsByTranscript - not recognized annotations
... The problem is not the UTR ranges (those are just ignored) but rather the absence of "exon" ranges. You'll need those for this to work. The GenomicFeatures maintainers might decide to support the utr + CDS way of specifying exons, but currently explicit "exon" ranges are required. ...
written 4 months ago by Michael Lawrence10.0k
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Comment: C: intronsByTranscript and fiveUTRsByTranscript - not recognized annotations
... The issue with the UTRs seems to be that the GenomicFeatures package ignores the three/five_prime_utr features and instead relies on exon features (and their difference from the CDS features). The GFF3 spec says: UTRs, splice sites and translational start and stop sites. These are implied by the ...
written 4 months ago by Michael Lawrence10.0k

Latest awards to Michael Lawrence

Scholar 11 months ago, created an answer that has been accepted. For A: setdiff for GenomicRanges
Scholar 11 months ago, created an answer that has been accepted. For A: Features within 2kb window, but with resampling
Scholar 11 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 11 months ago, created an answer that has been accepted. For A: reduce function after combining 2 GRanges objects from cn.mops output
Scholar 11 months ago, created an answer that has been accepted. For A: filtering VCF files
Scholar 11 months ago, created an answer that has been accepted. For A: Subset GRanges object into new object
Scholar 11 months ago, created an answer that has been accepted. For A: VariantAnnotation - expand not working as intended for VCF
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: closest-features equivalent in Bioconductor for finding closest gene(s)
Scholar 11 months ago, created an answer that has been accepted. For A: unlist a exons GRangeslist object and add a gene name column
Scholar 11 months ago, created an answer that has been accepted. For A: Genomic Ranges findOverlaps by sample
Scholar 11 months ago, created an answer that has been accepted. For A: Can rtracklayer import tab-delimited BED files with unquoted spaces in fields?
Teacher 11 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 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: Why export of empty GRanges to GFF fails?
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: annotate GRanges with upstream or downstream nearest gene
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: filtering VCF files
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: setdiff for GenomicRanges
Scholar 11 months ago, created an answer that has been accepted. For A: issue renaming seqnames in genomic ranges
Scholar 11 months ago, created an answer that has been accepted. For A: does import.bw with the selection argument take into account strand?
Scholar 11 months ago, created an answer that has been accepted. For A: VariantAnnotation as.vranges with asterisk in ALT field
Scholar 11 months ago, created an answer that has been accepted. For A: Group GRanges and keep metadata
Teacher 11 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 11 months ago, created a question with more than 1,000 views. For Job Opening: Computational Biologist @ Genentech Bioinformatics
Scholar 11 months ago, created an answer that has been accepted. For A: Detecting Overlaps within Grange Object

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