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srnadiff\"", "author": "Matthias Zytnicki, Ignacio González", "engine": "knitr::rmarkdown", "headings": [ "Version info", "Abstract", "Introduction", "Citing r Biocpkg(\"srnadiff\")", "How to get help for r Biocpkg(\"srnadiff\")", "Quick start", "Using r Biocpkg(\"srnadiff\")", "Installation", "Data overview", "Data preparation: the srnadiffExp object", "Content", "Adding an annotation", "Directionality", "The srnaExp object", "Read annotation", "Extraction of putative regions using an GTF annotation file", "Whole genome file annotation", "Extraction of precursor miRNAs using a miRBase-formatted GFF file", "Extraction of mature miRNAs using a miRBase-formatted GFF file", "Other format", "Performing sRNA-diff", "Working with the srnadiffExp object", "Extracting regions", "Data visualization", "Methods behind r Biocpkg(\"srnadiff\")", "Pre-processing data", "Methods to produce differentially expressed regions", "HMM method: hmm", "IR method: IR", "Naive method: naive", "Quantifying 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