Moderator: Michael Lawrence

gravatar for Michael Lawrence
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Posts by Michael Lawrence

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Comment: C: annotation of SV (Structural Variants)
... VariantAnnotation will give you the calls but I don't think we're annotating stuff at this level. locateVariants() would be a good place to start. ...
written 49 minutes ago by Michael Lawrence9.1k
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Comment: C: makeTxDbFromUCSC("hg38", "refGene") gives "not supported" error
... Seems like supportedUCSCtables() should look at tableNames(ucscTableQuery(session)) instead of names(trackNames(session)) when filtering.  ...
written 9 hours ago by Michael Lawrence9.1k
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Answer: A: pintersect and psetdiff changed behavior
... I am pretty sure those methods were moved to the intersect() and setdiff() generics, since the "p" is implied when operating over two lists. That's confused me in the past, too. ...
written 12 hours ago by Michael Lawrence9.1k
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Answer: A: filtering VCF files
... Maybe your expression could be something like: fs & sor | !isSNV(x)   ...
written 7 days ago by Michael Lawrence9.1k
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Comment: C: Importing Gene Symbols with makeTxDbFromGFF
... It's obviously unfortunate that the user starts with the gene names but then is forced to discard them and get them back. It would be nice if TxDb supported arbitrary meta columns, e.g., through a NoSQL or EAV approach. ...
written 7 days ago by Michael Lawrence9.1k
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Answer: A: rtracklayer: how to export gff file with gene names included?
... You probably want to use version 3 of the format, by using the extension "gff3" or specifying format="3". Otherwise, it uses GFF version 1 by default, which is limited and so old that I can't even find the spec anymore. ...
written 12 days ago by Michael Lawrence9.1k
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Comment: C: Combining RangedData objects is broken (IRanges 2.8.1 with R version 3.3.3 RC)
... I'm guessing something in your package library is out of sync. Might try reinstalling IRanges or its dependencies. ...
written 25 days ago by Michael Lawrence9.1k
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Comment: C: Accessing the BigWig files from the web
... Weird, my only guess is that it's some sort of locale issue.  ...
written 25 days ago by Michael Lawrence9.1k
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Answer: A: Why export of empty GRanges to GFF fails?
... Thanks, this should be fixed in version 1.35.7 (devel). ...
written 26 days ago by Michael Lawrence9.1k
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Answer: A: In ggbio, plot transcripts from a TxDb with gene labels
... The TxDb objects do not contain gene symbols (go figure). You could use an OrganismDb object (e.g., from the Homo.sapiens package). Then ggbio will use gene symbols by default. ...
written 26 days ago by Michael Lawrence9.1k

Latest awards to Michael Lawrence

Scholar 9 hours ago, created an answer that has been accepted. For A: filtering VCF files
Teacher 7 days ago, created an answer with at least 3 up-votes. For A: filtering VCF files
Scholar 7 days ago, created an answer that has been accepted. For A: filtering VCF files
Scholar 12 days ago, created an answer that has been accepted. For A: Genomic Ranges findOverlaps by sample
Scholar 25 days ago, created an answer that has been accepted. For A: Genomic Ranges findOverlaps by sample
Scholar 6 weeks ago, created an answer that has been accepted. For A: Genomic Ranges findOverlaps by sample
Scholar 7 weeks ago, created an answer that has been accepted. For A: Genomic Ranges findOverlaps by sample
Scholar 7 weeks ago, created an answer that has been accepted. For A: setdiff for GenomicRanges
Scholar 7 weeks ago, created an answer that has been accepted. For A: Genomic Ranges findOverlaps by sample
Scholar 7 weeks 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: setdiff between GenomicRanges objects keeping metadata
Scholar 11 months ago, created an answer that has been accepted. For A: Operations across Lists of GenomicRanges?
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Operations across Lists of GenomicRanges?
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: How to extract out wanted IntegerList more elegantly from nested list?
Scholar 11 months ago, created an answer that has been accepted. For A: filter "isSnp" for VCF
Scholar 11 months ago, created an answer that has been accepted. For A: Add main title to ggbio's karyogram
Scholar 11 months ago, created an answer that has been accepted. For A: export.bw produces enormous files (10^5 times bigger than they should be)
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: How to find particular types of overlap with GenomicRanges
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: How to use GenomicRanges to find overlaps by percentage covered of interval
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: parRapply in BiocParallel ?
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Combining two GRangesLists
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Collapse/Reduce in GRanges by Metadata Column
Scholar 11 months ago, created an answer that has been accepted. For A: "duplicated" on LogicalList with fromLast = TRUE gives error
Scholar 11 months ago, created an answer that has been accepted. For A: Proper way to read in a DataFrame with CharacterList columns that was saved to a

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