├── .DS_Store ├── .Rbuildignore ├── .Rhistory ├── .gitignore ├── DESCRIPTION ├── NAMESPACE ├── R ├── .DS_Store ├── ADstat.hy.R ├── ADstatWins.hy.R ├── PCnum.gamma.hy.R ├── RNAcurve.R ├── RNAcurveOne.R ├── Relist.hy.R ├── Scissor.R ├── SlogADstat.hy.R ├── adj.center.R ├── angle.hy.R ├── bisquare.sse.R ├── build_gaf.R ├── build_pileup.R ├── center_data.R ├── check_normals.R ├── compScales.R ├── decay.rate.hy.R ├── estimate_offset.R ├── fastSplitSample.R ├── find.exon.hy.R ├── generdir.R ├── getShiftParam.R ├── get_PO.R ├── get_Ranges.R ├── get_junctions.R ├── get_sparsePD4one.R ├── get_splicedReads.R ├── interpolate.hy.R ├── junction_outliers.R ├── kdeplot.hy.R ├── len.intron.hy.R ├── lm.pval.R ├── logtransform_data.R ├── miscGlobal.R ├── miscLocal.R ├── normalize_data.R ├── palette_SCISSOR.R ├── pca.hy.R ├── pca2misc.R ├── pd.rate.hy.R ├── plot_ScissorOS.R ├── plot_ScissorSC.R ├── plot_offset.R ├── plot_pileup.R ├── pos.sd.R ├── process_pileup.R ├── read_BAM.R ├── resmat.outliers.hy.R ├── rhoHuber.R ├── scale.factor.R ├── scale1StepM.R └── yaxis.hy.R ├── README.md ├── SCISSOR.Rproj ├── data ├── .DS_Store ├── TOY_coverage.txt └── TOY_data.RData ├── docs ├── .DS_Store ├── about.md ├── example.md ├── images │ ├── TOY_OS_kdeplot.png │ ├── TOY_log.png │ ├── TOY_raw.png │ ├── TOY_raw_pileup.png │ └── TOY_results.png ├── index.md ├── installation.md └── tutorial.md ├── man ├── ADstat.hy.Rd ├── ADstatWins.hy.Rd ├── PCnum.gamma.hy.Rd ├── RNAcurve.Rd ├── Scissor.Rd ├── adj.center.Rd ├── build_gaf.Rd ├── build_pileup.Rd ├── center_data.Rd ├── detect_localout.Rd ├── find.exon.hy.Rd ├── generdir.Rd ├── getShiftParam.Rd ├── get_Ranges.Rd ├── get_SRcount.Rd ├── get_offstat.Rd ├── get_sparsePD4one.Rd ├── kdeplot.hy.Rd ├── len.intron.hy.Rd ├── logtransform_data.Rd ├── miscGlobal.Rd ├── miscLocal.Rd ├── normalize_data.Rd ├── palette_SCISSOR.Rd ├── pd.rate.hy.Rd ├── plot_ScissorOS.Rd ├── plot_ScissorSC.Rd ├── plot_pileup.Rd ├── process_pileup.Rd ├── read_BAM.Rd └── scale.factor.Rd ├── mkdocs.yml └── site ├── about └── index.html ├── css ├── theme.css └── theme_extra.css ├── example └── index.html ├── fonts ├── Lato │ ├── lato-bold.eot │ ├── lato-bold.ttf │ ├── lato-bold.woff │ ├── lato-bold.woff2 │ ├── lato-bolditalic.eot │ ├── lato-bolditalic.ttf │ ├── lato-bolditalic.woff │ ├── lato-bolditalic.woff2 │ ├── lato-italic.eot │ ├── lato-italic.ttf │ ├── lato-italic.woff │ ├── lato-italic.woff2 │ ├── lato-regular.eot │ ├── lato-regular.ttf │ ├── lato-regular.woff │ └── lato-regular.woff2 ├── RobotoSlab │ ├── roboto-slab-v7-bold.eot │ ├── roboto-slab-v7-bold.ttf │ ├── roboto-slab-v7-bold.woff │ ├── roboto-slab-v7-bold.woff2 │ ├── roboto-slab-v7-regular.eot │ ├── roboto-slab-v7-regular.ttf │ ├── roboto-slab-v7-regular.woff │ ├── roboto-slab-v7-regular.woff2 │ └── roboto-slab.eot ├── fontawesome-webfont.eot ├── fontawesome-webfont.svg ├── fontawesome-webfont.ttf ├── fontawesome-webfont.woff └── fontawesome-webfont.woff2 ├── images ├── TOY_OS_kdeplot.png ├── TOY_log.png ├── 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