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"_vignettes": [ { "source": "IntEREst.Rmd", "filename": "IntEREst.html", "title": "IntEREst", "author": "Ali Oghabian", "engine": "knitr::rmarkdown", "headings": [ "Introduction to IntEREst", "Creating reference", "Building GFF3 file", "Extracting U12 introns info from 'u12' data", "Building reference", "Intron retention, Inton spanning and exon-exon junction level estimation", "Using the test data mdsChr22Obj", "See read counts", "See FPKM Normalized values", "See intron/exon annotations", "See sample annotations", "Comparing intron retention levels across various samples", "Run exact test", "Number of stabilized introns (in Chr 22)", "Number of stabilized (significantly retained) U12 type introns", "Number of U12 introns", "Fraction(%) of stabilized (significantly retained) U12 introns", "Number of stabilized U2 type introns", "Number of U2 introns", "Fraction(%) of stabilized U2 introns", "Our recommended pipeline for differential intron retention analysis", "References" ], 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