User: Devin King

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Devin King20
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Posts by Devin King

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Implementing fast mathematical and statistical operations on genomic variables in bioconductor
... The current paradigm to represent genomic variables (e.g. ChIP-seq coverage) in Bioconductor is as a named RleList or as a metadata column on a disjoint GRanges object. This can provide remarkable functionality and performance. However, how does one properly implement mathematical or statistical ope ...
iranges genomicranges biocgenerics rlelist genomicvars written 4 months ago by Devin King20 • updated 4 months ago by Hervé Pagès ♦♦ 13k
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Comment: C: Possible issue with Rsamtools ScanBamParam mapqfilter
... Hi Hervé,   Thank you for your response, I apologize I haven't responded sooner. Here is a download link to a small bam file (2.9 Mb) and its associated bam index. The BAM is a sampling of about 15,000 PE reads on chromosome 1 (mapped with BWA to hg19). The index was created with Rsamtools:::index ...
written 5 months ago by Devin King20
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Possible issue with Rsamtools ScanBamParam mapqfilter
... I'm having an issue importing (part of) a BAM file into R using the Rsamtools readGAlignmentPairs() function. In particular, I raise a peculiar error ("subscript contains NAs") when using a ScanBamParam object with bamMapqFilter set to not NA and > 0.  This only happens with some BAM files, so it ...
rsamtools scanbamparam mapqfilter written 6 months ago by Devin King20

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