├── .Rprofile ├── .gitignore ├── README.md ├── _workflowr.yml ├── analysis ├── _site.yml ├── about.Rmd ├── index.Rmd ├── license.Rmd ├── scRNAseq_workshop_0.Rmd ├── scRNAseq_workshop_1.Rmd ├── scRNAseq_workshop_2.Rmd ├── scRNAseq_workshop_3.Rmd └── scRNAseq_workshop_4.Rmd ├── code └── README.md ├── data └── README.md ├── docs ├── .nojekyll ├── about.html ├── assets │ ├── Run_folder.png │ ├── iSEE.png │ └── msigdb.png ├── figure │ ├── scRNAseq_workshop_1.Rmd │ │ ├── unnamed-chunk-14-1.png │ │ ├── unnamed-chunk-15-1.png │ │ ├── unnamed-chunk-15-2.png │ │ ├── unnamed-chunk-17-1.png │ │ ├── unnamed-chunk-18-1.png │ │ ├── unnamed-chunk-18-2.png │ │ ├── unnamed-chunk-20-1.png │ │ ├── unnamed-chunk-20-2.png │ │ ├── unnamed-chunk-20-3.png │ │ ├── unnamed-chunk-21-1.png │ │ ├── unnamed-chunk-21-2.png │ │ ├── unnamed-chunk-25-1.png │ │ ├── unnamed-chunk-26-1.png │ │ ├── unnamed-chunk-26-2.png │ │ ├── unnamed-chunk-27-1.png │ │ ├── unnamed-chunk-28-1.png │ │ ├── unnamed-chunk-28-2.png │ │ ├── unnamed-chunk-29-1.png │ │ ├── unnamed-chunk-6-1.png │ │ └── unnamed-chunk-9-1.png │ ├── scRNAseq_workshop_2.Rmd │ │ ├── unnamed-chunk-10-1.png │ │ ├── unnamed-chunk-11-1.png │ │ ├── unnamed-chunk-12-1.png │ │ ├── unnamed-chunk-4-1.png │ │ ├── unnamed-chunk-6-1.png │ │ ├── unnamed-chunk-7-1.png │ │ └── unnamed-chunk-9-1.png │ └── scRNAseq_workshop_3.Rmd │ │ ├── unnamed-chunk-5-1.png │ │ └── unnamed-chunk-6-1.png ├── img │ ├── Run_folder.png │ ├── iSEE.png │ └── msigdb.png ├── index.html ├── license.html ├── scRNAseq_workshop_0.html ├── scRNAseq_workshop_1.html ├── scRNAseq_workshop_2.html ├── scRNAseq_workshop_3.html ├── scRNAseq_workshop_4.html ├── site_libs │ ├── 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 │ │ │ ├── darkly.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 │ ├── font-awesome-5.1.0 │ │ ├── css │ │ │ ├── all.css │ │ │ └── v4-shims.css │ │ └── webfonts │ │ │ ├── fa-brands-400.eot │ │ │ ├── fa-brands-400.svg │ │ │ ├── fa-brands-400.ttf │ │ │ ├── fa-brands-400.woff │ │ │ ├── fa-brands-400.woff2 │ │ │ ├── fa-regular-400.eot │ │ │ ├── fa-regular-400.svg │ │ │ ├── fa-regular-400.ttf │ │ │ ├── fa-regular-400.woff │ │ │ ├── fa-regular-400.woff2 │ │ │ ├── fa-solid-900.eot │ │ │ ├── fa-solid-900.svg │ │ │ ├── fa-solid-900.ttf │ │ │ ├── fa-solid-900.woff │ │ │ └── fa-solid-900.woff2 │ ├── highlightjs-9.12.0 │ │ ├── default.css │ │ ├── highlight.js │ │ └── textmate.css │ ├── jquery-1.11.3 │ │ └── jquery.min.js │ ├── jqueryui-1.11.4 │ │ ├── README │ │ ├── images │ │ │ ├── ui-icons_444444_256x240.png │ │ │ ├── ui-icons_555555_256x240.png │ │ │ ├── ui-icons_777620_256x240.png │ │ │ ├── ui-icons_777777_256x240.png │ │ │ ├── ui-icons_cc0000_256x240.png │ │ │ └── ui-icons_ffffff_256x240.png │ │ ├── index.html │ │ ├── jquery-ui.css │ │ ├── jquery-ui.js │ │ ├── jquery-ui.min.css │ │ ├── jquery-ui.min.js │ │ ├── jquery-ui.structure.css │ │ ├── jquery-ui.structure.min.css │ │ ├── jquery-ui.theme.css │ │ └── jquery-ui.theme.min.css │ ├── navigation-1.1 │ │ ├── codefolding.js │ │ ├── sourceembed.js │ │ └── tabsets.js │ └── tocify-1.9.1 │ │ ├── jquery.tocify.css │ │ └── jquery.tocify.js └── welcome_umap.png ├── output └── README.md └── scRNA-seq-workshop-Fall-2019.Rproj /.Rprofile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/crazyhottommy/scRNA-seq-workshop-Fall-2019/HEAD/.Rprofile -------------------------------------------------------------------------------- /.gitignore: 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