Moderator: Michael Lawrence

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Posts by Michael Lawrence

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Answer: A: browseGenome with Shiny
... Version 1.41.8 supports passing browse=FALSE to browserView() to prevent browsing to the URL. Get the URL from the returned view object with viewURL(). ...
written 3 hours ago by Michael Lawrence10k
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Comment: C: browseGenome with Shiny
... I guess the view constructor could be instructed not to show/browse itself but instead keep the information in a slot that could be queried to get the URL. Then you could pass that argument down through browseGenome() although it might be better to just construct the session and view directly. ...
written 1 day ago by Michael Lawrence10k
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Comment: C: GenomicRanges based on indices or more conditions, and add column from match
... This is basically an inner join, but then reducing the data so that no rows in df1 become repeated. How do you want to reduce the data when one row in df1 overlaps more than one row in df2? ...
written 1 day ago by Michael Lawrence10k
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Comment: C: GenomicRanges based on indices or more conditions, and add column from match
... Not sure I understand your example. But I think you could get further using intersect(hits1, hits2), which would find the rows where df1 overlaps df2 and df3 overlaps df4.   ...
written 1 day ago by Michael Lawrence10k
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Comment: C: ggbio labels with ggrepeal on circos plot
... Probably best to open a GitHub issue and @-in the ggrepel people. ...
written 12 days ago by Michael Lawrence10k
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Comment: C: Selecting columns form a list of grange objects
... Are you looping over the list? Like GRangesList(lapply(data_bed, function(x) x[,"name"]))? ...
written 18 days ago by Michael Lawrence10k
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Answer: A: Selecting columns form a list of grange objects
... On a single GRanges, you could do something like x[,"name"]. Just do that over the whole list. ...
written 20 days ago by Michael Lawrence10k
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Comment: C: aes label in ggbio_1.26.1 with ggplot2_3.0.0
... Please update your R/Bioconductor and see if the problem persists. If it does, please let me know how you constructed "myGR". ...
written 27 days ago by Michael Lawrence10k
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Answer: A: rtracklayer export bedGraph cannot be loaded into UCSC
... bedGraph (at least as strictly defined by what UCSC supports) does not support overlapping intervals. The bug is that rtracklayer fails  silently to produce bedGraph and instead produces BED. For your work, you will need to aggregate the data so that they can be displayed in UCSC correctly. ...
written 5 weeks ago by Michael Lawrence10k
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Comment: C: rtracklayer export bedGraph cannot be loaded into UCSC
... Alright, please send a reproducible example, i.e., include the input data. ...
written 5 weeks ago by Michael Lawrence10k

Latest awards to Michael Lawrence

Scholar 4 months ago, created an answer that has been accepted. For A: Detecting Overlaps within Grange Object
Scholar 4 months ago, created an answer that has been accepted. For A: Features within 2kb window, but with resampling
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: trying to annotate overlaps with external file information
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: setdiff for GenomicRanges
Scholar 15 months ago, created an answer that has been accepted. For A: filtering VCF files
Scholar 15 months ago, created an answer that has been accepted. For A: Subset GRanges object into new object
Scholar 15 months ago, created an answer that has been accepted. For A: Features within 2kb window, but with resampling
Scholar 15 months ago, created an answer that has been accepted. For A: closest-features equivalent in Bioconductor for finding closest gene(s)
Scholar 15 months ago, created an answer that has been accepted. For A: reduce function after combining 2 GRanges objects from cn.mops output
Scholar 15 months ago, created an answer that has been accepted. For A: unlist a exons GRangeslist object and add a gene name column
Scholar 15 months ago, created an answer that has been accepted. For A: Genomic Ranges findOverlaps by sample
Scholar 15 months ago, created an answer that has been accepted. For A: Can rtracklayer import tab-delimited BED files with unquoted spaces in fields?
Teacher 15 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 15 months ago, created an answer that has been accepted. For A: trying to annotate overlaps with external file information
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: filtering VCF files
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: trying to annotate overlaps with external file information
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: annotate GRanges with upstream or downstream nearest gene
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: setdiff for GenomicRanges
Scholar 15 months ago, created an answer that has been accepted. For A: issue renaming seqnames in genomic ranges
Scholar 15 months ago, created an answer that has been accepted. For A: does import.bw with the selection argument take into account strand?
Scholar 15 months ago, created an answer that has been accepted. For A: VariantAnnotation as.vranges with asterisk in ALT field
Scholar 15 months ago, created an answer that has been accepted. For A: Group GRanges and keep metadata
Teacher 15 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?
Scholar 15 months ago, created an answer that has been accepted. For A: Why export of empty GRanges to GFF fails?
Scholar 15 months ago, created an answer that has been accepted. For A: VariantAnnotation - expand not working as intended for VCF

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