├── .Rbuildignore ├── .gitignore ├── .travis.yml ├── DESCRIPTION ├── NAMESPACE ├── NEWS ├── R ├── MotifSetup-class.R ├── PlotSetArray-class.R ├── PlotSetList-class.R ├── PlotSetPair-class.R ├── add_local_files.R ├── deployServerInstance.R ├── generic_methods.R ├── getPlotSetArray.R ├── helper_functions.R ├── int_getSF.R ├── int_ggHeatmapPlotWrapper.R ├── int_heatmapPlotWrapper.R ├── int_imPlot2.R ├── int_plotMext.R ├── plotAverage.R ├── plotHeatmap.R ├── run.R ├── seqplots-package.R └── zzz.R ├── README.md ├── SeqPlots_Rpackage.Rproj ├── appveyor.yml ├── codecov.yml ├── index.html ├── inst ├── CITATION ├── extdata │ ├── GSM1208360_chrI_100Kb_q5_sample.bw │ ├── GSM1208361_chrI_100Kb_PeakCalls.bed │ ├── Transcripts_ce10_chrI_100Kb.bed │ └── precalc_plotset.Rdata ├── extdocs │ ├── Logo.R │ ├── pkgdown.R │ └── source_control.md └── seqplots │ ├── functions │ ├── LOCAL │ │ ├── mceval.R │ │ ├── server_plotHeatmap.R │ │ └── server_plotLineplot.R │ ├── doFileOperations.R │ ├── mcCalcStart_calculations.R │ ├── mcDoParallel_plotting.R │ └── renderHTMLgrid.R │ ├── global.R │ ├── server.R │ ├── server_config.R │ ├── ui.R │ ├── ui │ ├── DataTablesColumnSetup.js │ ├── DataTablesToolsSetup.js │ ├── FileManagementModal.R │ └── loadModal.html │ └── www │ ├── biodalliance.html │ ├── color │ ├── arrow.gif │ ├── cross.gif │ ├── hs.png │ ├── hv.png │ └── jscolor.js │ ├── css │ ├── DT_bootstrap.css │ ├── NewFont.woff │ ├── TableTools.css │ ├── font-awesome.min.css │ ├── images │ │ ├── back_disabled.png │ │ ├── back_enabled.png │ │ ├── back_enabled_hover.png │ │ ├── forward_disabled.png │ │ ├── forward_enabled.png │ │ ├── forward_enabled_hover.png │ │ ├── sort_asc.png │ │ ├── sort_asc_disabled.png │ │ ├── sort_both.png │ │ ├── sort_desc.png │ │ └── sort_desc_disabled.png │ ├── mask2.png │ └── style.css │ ├── font │ ├── FontAwesome.otf │ ├── fontawesome-webfont.eot │ ├── fontawesome-webfont.svg │ ├── fontawesome-webfont.ttf │ └── fontawesome-webfont.woff │ ├── help │ ├── AdvOup.md │ ├── Batch.md │ ├── Errors.md │ ├── Files.md │ ├── GUIplottingControls.md │ ├── Genomes.md │ ├── Heatmaps.md │ ├── Home.md │ ├── Home2.md │ ├── Install_Docker.md │ ├── Install_OSX.md │ ├── Install_R.md │ ├── Install_apps.md │ ├── Install_server.md │ ├── Legacy.md │ ├── Outputs.md │ ├── PlotSets.md │ ├── Plotting.md │ ├── QuickStart.md │ ├── References.md │ ├── SaveAndLoad.md │ ├── Terms.md │ ├── Versions.md │ ├── help.Rmd │ ├── help.html │ ├── help_files │ │ ├── bootstrap-3.3.5 │ │ │ ├── css │ │ │ │ ├── bootstrap-theme.css │ │ │ │ ├── bootstrap-theme.css.map │ │ │ │ ├── bootstrap-theme.min.css │ │ │ │ ├── bootstrap.css │ │ │ │ ├── bootstrap.css.map │ │ │ │ ├── bootstrap.min.css │ │ │ │ ├── cerulean.min.css │ │ │ │ ├── cosmo.min.css │ │ │ │ ├── flatly.min.css │ │ │ │ ├── fonts │ │ │ │ │ ├── Lato.ttf │ │ │ │ │ ├── LatoBold.ttf │ │ │ │ │ ├── LatoItalic.ttf │ │ │ │ │ ├── NewsCycle.ttf │ │ │ │ │ ├── NewsCycleBold.ttf │ │ │ │ │ ├── OpenSans.ttf │ │ │ │ │ ├── OpenSansBold.ttf │ │ │ │ │ ├── OpenSansBoldItalic.ttf │ │ │ │ │ ├── OpenSansItalic.ttf │ │ │ │ │ ├── OpenSansLight.ttf │ │ │ │ │ ├── OpenSansLightItalic.ttf │ │ │ │ │ ├── Raleway.ttf │ │ │ │ │ ├── RalewayBold.ttf │ │ │ │ │ ├── Roboto.ttf │ │ │ │ │ ├── RobotoBold.ttf │ │ │ │ │ ├── RobotoLight.ttf │ │ │ │ │ ├── RobotoMedium.ttf │ │ │ │ │ ├── SourceSansPro.ttf │ │ │ │ │ ├── SourceSansProBold.ttf │ │ │ │ │ ├── SourceSansProItalic.ttf │ │ │ │ │ ├── SourceSansProLight.ttf │ │ │ │ │ └── Ubuntu.ttf │ │ │ │ ├── journal.min.css │ │ │ │ ├── lumen.min.css │ │ │ │ ├── paper.min.css │ │ │ │ ├── readable.min.css │ │ │ │ ├── sandstone.min.css │ │ │ │ ├── simplex.min.css │ │ │ │ ├── spacelab.min.css │ │ │ │ ├── united.min.css │ │ │ │ └── yeti.min.css │ │ │ ├── fonts │ │ │ │ ├── glyphicons-halflings-regular.eot │ │ │ │ ├── glyphicons-halflings-regular.svg │ │ │ │ ├── glyphicons-halflings-regular.ttf │ │ │ │ ├── glyphicons-halflings-regular.woff │ │ │ │ └── glyphicons-halflings-regular.woff2 │ │ │ ├── js │ │ │ │ ├── bootstrap.js │ │ │ │ ├── bootstrap.min.js │ │ │ │ └── npm.js │ │ │ └── shim │ │ │ │ ├── html5shiv.min.js │ │ │ │ └── respond.min.js │ │ ├── jquery-1.11.3 │ │ │ └── jquery.min.js │ │ └── navigation-1.1 │ │ │ ├── FileSaver.min.js │ │ │ ├── codefolding.js │ │ │ ├── sourceembed.js │ │ │ └── tabsets.js │ ├── img │ │ ├── 01_QuickStart │ │ │ ├── 01_QuickStart_01.png │ │ │ ├── 01_QuickStart_02.png │ │ │ ├── 01_QuickStart_03.png │ │ │ ├── 01_QuickStart_04.png │ │ │ ├── 01_QuickStart_05.png │ │ │ ├── 01_QuickStart_06.png │ │ │ ├── 01_QuickStart_07.png │ │ │ ├── 01_QuickStart_08.png │ │ │ ├── 01_QuickStart_09.png │ │ │ ├── 01_QuickStart_10.png │ │ │ ├── 01_QuickStart_11.png │ │ │ └── 01_QuickStart_12.png │ │ ├── 03_01.png │ │ ├── 03_01a.png │ │ ├── 03_01b.png │ │ ├── 03_02.png │ │ ├── 03_03.png │ │ ├── 03_04.png │ │ ├── 05_01.png │ │ ├── 05_02.png │ │ ├── 05_03.png │ │ ├── 05_04.png │ │ ├── 06 │ │ │ ├── 06_01.png │ │ │ ├── 06_02.png │ │ │ ├── 06_03.png │ │ │ └── 06_04.png │ │ ├── 07_01.png │ │ ├── 07_02.png │ │ ├── 07_03.png │ │ ├── 07_04.png │ │ ├── 07_05_06.png │ │ ├── 08_01.png │ │ ├── 08_02.png │ │ ├── 08_03.png │ │ ├── 08_04.png │ │ ├── 08_05.png │ │ ├── 09_01.png │ │ ├── 09_02.png │ │ ├── 09_03.png │ │ ├── 09_04.png │ │ ├── 10_00.png │ │ ├── 10_01.png │ │ ├── 11_01.png │ │ ├── SeqPlots_fig1_web.png │ │ ├── fav.ico │ │ ├── ico_full.png │ │ ├── ico_full_color.png │ │ ├── palettes.png │ │ ├── seqplots_sticker.png │ │ └── seqplots_sticker_bl.png │ ├── style.css │ ├── template2.html │ └── topbar.html │ ├── js │ ├── DataTables │ │ ├── DT_bootstrap.js │ │ ├── DT_filter.js │ │ ├── dataTables.tableTools.min.js │ │ └── jquery.dataTables.js │ ├── actionbutton.js │ ├── afterHTMLgridrender.js │ ├── color.js │ ├── jquery.ba-throttle-debounce.js │ ├── jquery.cookie.js │ ├── jquery.lettering.js │ ├── js_addons.js │ ├── load_finished.js │ ├── modal_events.js │ ├── pdf.js │ ├── pdf.worker.js │ ├── tmpl.min.js │ └── tutorial.js │ ├── outro.html │ ├── tutorial.html │ └── upload │ ├── css │ ├── jquery.fileupload-ui-noscript.css │ ├── jquery.fileupload-ui.css │ └── style.css │ ├── img │ ├── loading.gif │ └── progressbar.gif │ ├── js │ ├── cors │ │ ├── jquery.postmessage-transport.js │ │ └── jquery.xdr-transport.js │ ├── jquery.fileupload-fp.js │ ├── jquery.fileupload-ui.js │ ├── jquery.fileupload-validate.js │ ├── jquery.fileupload.js │ ├── jquery.iframe-transport.js │ ├── main.js │ ├── md5.js │ └── vendor │ │ └── jquery.ui.widget.js │ └── upload.html ├── man ├── MotifSetup-class.Rd ├── PlotSetArray-class.Rd ├── PlotSetList-class.Rd ├── PlotSetPair-class.Rd ├── add_local_file.Rd ├── deployServerInstance.Rd ├── getPlotSetArray.Rd ├── getREF.Rd ├── ggHeatmapPlotWrapper.Rd ├── heatmapPlotWrapper.Rd ├── imPlot2.Rd ├── import.narrowPeak.Rd ├── num2bp.Rd ├── num2sci.Rd ├── plot.Rd ├── plotAverage.Rd ├── plotHeatmap.Rd ├── plotMext.Rd ├── run.Rd ├── seqplots-generic.Rd └── seqplots.Rd ├── tests ├── test-all.R └── testthat │ └── test1.R └── vignettes ├── QuickStart.Rmd └── 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