|bam.cov.gr||Get coverage as GRanges from BAM on custom set of GRanges|
|bam.cov.tile||Get coverage as GRanges from BAM on genome tiles across...|
|bamflag||Returns matrix of bits from BAM flags|
|bamtag||Outputs a tag to identify duplicate reads in GRanges input|
|countCigar||Count bases in cigar string|
|count.clips||Return data.frame with fields of "right" soft clips and...|
|get.mate.gr||returns GRanges corresponding to mates of reads|
|get.pairs.grl||Get coverage as GRanges from BAM on custom set of GRanges|
|is.paired.end||Check if BAM file is paired end by using 0x1 flag|
|mafcount||Wrapper around varcount adapted to tumor and normal "paired"...|
|read.bam||Read BAM file into GRanges or data.table|
|splice.cigar||Get coverage as GRanges from BAM on custom set of GRanges|
|varbase||Returns variant bases and ranges from GRanges or...|
|varcount||Wrapper around applyPileups|
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