Moderator: Michael Lawrence

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Posts by Michael Lawrence

<prev • 1,328 results • page 1 of 133 • next >
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Comment: C: rtracklayer export bedGraph cannot be loaded into UCSC
... Please note that the GRanges (and IRanges) convention is that ranges are 1-based, inclusive. rtracklayer just follows that convention. ...
written 2 days ago by Michael Lawrence11k
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Answer: A: negative AD value interfering with readVcfasVRanges
... Best to ask the maintainer of whatever generated the VCF file. ...
written 5 days ago by Michael Lawrence11k
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Answer: A: Assesing genomic segment enrichment with GenomicRanges (R-package)
... To treat ranges as sets, look at the Ranges methods for `setdiff()`, `intersect()` and `union()`. ...
written 22 days ago by Michael Lawrence11k
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Answer: A: DataFrame after splitting and back
... In devel there is a new `recursive=TRUE` argument on `expand()` that if `FALSE` will expand columns in parallel, so you can now do: ``` expand(df2, recursive=FALSE) ``` as long as you don't care that the data are sorted by "k". ...
written 9 weeks ago by Michael Lawrence11k
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Comment: C: How to tell a GAlignmentsList singleton is mate1 or mate2
... Could use the flag utilities like `bamFlagAsBitMatrix()` and `bamFlagTest()`. ...
written 11 weeks ago by Michael Lawrence11k
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Comment: C: Aggregating scores of multiple metadata columns from one GRanges object on anoth
... I edited by answer to include the call to `bindROWS()` but I'm not sure if it will work. Please provide a fully reproducible example. ...
written 12 weeks ago by Michael Lawrence11k
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Comment: C: Aggregating scores of multiple metadata columns from one GRanges object on anoth
... mcols(x)$scores <- mat ...
written 12 weeks ago by Michael Lawrence11k
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Comment: C: Aggregating scores of multiple metadata columns from one GRanges object on anoth
... Add it as a column after construction. ...
written 12 weeks ago by Michael Lawrence11k
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Answer: A: Aggregating scores of multiple metadata columns from one GRanges object on anoth
... If you have thousands of score columns, you might find it more convenient to bind them into a matrix, stored as a single column on the GRanges. Then you could use the matrixStats package to compute the maxima across all columns. I think the code would look something like: ``` aggregate(tomap, hits, ...
written 12 weeks ago by Michael Lawrence11k
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Answer: A: RSBML wrong edges
... Cell Designer uses a different graph representation of the SBML model. The rsbml package generates a bipartite graph connecting species to reactions. The "re" identifiers refer to reactions. It sounds like Cell Designer is directly connecting reaction participants. You could collapse the rsbml graph ...
written 12 weeks ago by Michael Lawrence11k

Latest awards to Michael Lawrence

Scholar 5 months ago, created an answer that has been accepted. For A: Detecting Overlaps within Grange Object
Scholar 7 months ago, created an answer that has been accepted. For A: Detecting Overlaps within Grange Object
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: trying to annotate overlaps with external file information
Scholar 13 months ago, created an answer that has been accepted. For A: Detecting Overlaps within Grange Object
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: trying to annotate overlaps with external file information
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: setdiff for GenomicRanges
Scholar 13 months ago, created an answer that has been accepted. For A: Features within 2kb window, but with resampling
Scholar 24 months ago, created an answer that has been accepted. For A: Subset GRanges object into new object
Scholar 24 months ago, created an answer that has been accepted. For A: filtering VCF files
Scholar 24 months ago, created an answer that has been accepted. For A: Features within 2kb window, but with resampling
Scholar 24 months ago, created an answer that has been accepted. For A: Genomic Ranges findOverlaps by sample
Scholar 24 months ago, created an answer that has been accepted. For A: Can rtracklayer import tab-delimited BED files with unquoted spaces in fields?
Teacher 24 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 24 months ago, created an answer that has been accepted. For A: trying to annotate overlaps with external file information
Scholar 24 months ago, created an answer that has been accepted. For A: unlist a exons GRangeslist object and add a gene name column
Scholar 24 months ago, created an answer that has been accepted. For A: closest-features equivalent in Bioconductor for finding closest gene(s)
Scholar 24 months ago, created an answer that has been accepted. For A: reduce function after combining 2 GRanges objects from cn.mops output
Teacher 24 months ago, created an answer with at least 3 up-votes. For A: setdiff for GenomicRanges
Scholar 24 months ago, created an answer that has been accepted. For A: issue renaming seqnames in genomic ranges
Scholar 24 months ago, created an answer that has been accepted. For A: does import.bw with the selection argument take into account strand?
Scholar 24 months ago, created an answer that has been accepted. For A: VariantAnnotation as.vranges with asterisk in ALT field
Scholar 24 months ago, created an answer that has been accepted. For A: Group GRanges and keep metadata
Teacher 24 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?
Teacher 24 months ago, created an answer with at least 3 up-votes. For A: filtering VCF files
Teacher 24 months ago, created an answer with at least 3 up-votes. For A: trying to annotate overlaps with external file information

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