Scissor: All-in-one function for identifying shape changes in RNA-seq...
In hyochoi/Scissors:

All-in-one function for identifying shape changes in RNA-seq expression profile at a single gene

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Scissor(pileup, exon, siglev = 1e-04, logshift.val = 10,
  window.size = 50, input.type = "part_intron",
  output.type = "part_intron", normalization.plot = TRUE)

`pileup`	a pile-up data matrix obtained from bam files, i.e. base-level raw counts. Columns are samples and rows are genomic positions.
`exon`	an exon annotation for the given gene.
`siglev`	a significance level for detecting outliers. Default is 1e-4.
`logshift.val`	a pseudo count added to raw counts before the logarithmic transformation.
`window.size`	a window size used in the local shape change detection.
`input.type`	type of intronic region contained in pileup, with choices "whole_intron", "part_intron", or "only_exon"; the first is the default.
`output.type`	type of intronic region that will be included in output, with choices "whole_intron", "part_intron", or "only_exon"; the second is the default.
`normalization.plot`	logical, whether to plot variation with respect to overall expression with fitted curve. Default is FALSE