├── .Rprofile ├── .gitignore ├── README.md ├── _workflowr.yml ├── analysis ├── 10xv2.Rmd ├── 10xv3.Rmd ├── _site.yml ├── about.Rmd ├── index.Rmd ├── license.Rmd ├── monocle2.Rmd ├── monocle3.Rmd ├── slingshot.Rmd └── velocity.Rmd ├── code └── README.md ├── data └── README.md ├── docs ├── .nojekyll ├── 10xv2.html ├── 10xv3.html ├── about.html ├── figure │ ├── 10xv2.Rmd │ │ ├── barn-1.png │ │ ├── elbow-1.png │ │ ├── pca-1.png │ │ ├── rank-1.png │ │ ├── tsne-1.png │ │ ├── unnamed-chunk-20-1.png │ │ └── vln-1.png │ ├── 10xv3.Rmd │ │ ├── elbow-1.png │ │ ├── pca-1.png │ │ ├── rank-1.png │ │ ├── tsne-1.png │ │ ├── unnamed-chunk-13-1.png │ │ └── vln-1.png │ ├── monocle2.Rmd │ │ ├── knee-1.png │ │ ├── traj1-1.png │ │ ├── traj2-1.png │ │ ├── traj3-1.png │ │ ├── tsne1-1.png │ │ ├── tsne2-1.png │ │ ├── unnamed-chunk-20-1.png │ │ ├── unnamed-chunk-21-1.png │ │ └── unnamed-chunk-22-1.png │ ├── monocle3.Rmd │ │ ├── elbow-1.png │ │ ├── genes-1.png │ │ ├── part-1.png │ │ ├── pca-1.png │ │ ├── pseudo-1.png │ │ ├── ti-1.png │ │ ├── umap-1.png │ │ └── unnamed-chunk-8-1.png │ ├── slingshot.Rmd │ │ ├── curves-1.png │ │ ├── elbow-1.png │ │ ├── genes-1.png │ │ ├── lin1-1.png │ │ ├── lin2-1.png │ │ ├── pca-1.png │ │ ├── pt-1.png │ │ ├── qc-1.png │ │ ├── tsne-1.png │ │ ├── umap-1.png │ │ ├── umap_clust-1.png │ │ └── vln-1.png │ └── velocity.Rmd │ │ ├── elbow-1.png │ │ ├── knee-1.png │ │ ├── pairs-1.png │ │ ├── pca-1.png │ │ ├── phase1-1.png │ │ ├── phase2-1.png │ │ ├── phase3-1.png │ │ ├── tsne-1.png │ │ ├── umap-1.png │ │ ├── umap_clust-1.png │ │ ├── unnamed-chunk-43-1.png │ │ ├── v1b-1.png │ │ └── v2-1.png ├── index.html ├── license.html ├── monocle2.html ├── monocle3.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 │ ├── crosstalk-1.0.0 │ │ ├── css │ │ │ └── crosstalk.css │ │ └── js │ │ │ ├── crosstalk.js │ │ │ ├── crosstalk.js.map │ │ │ ├── crosstalk.min.js │ │ │ └── crosstalk.min.js.map │ ├── 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 │ ├── htmlwidgets-1.5.1 │ │ └── htmlwidgets.js │ ├── 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 │ ├── plotly-binding-4.9.1 │ │ └── plotly.js │ ├── plotly-htmlwidgets-css-1.49.4 │ │ └── plotly-htmlwidgets.css │ ├── plotly-main-1.49.4 │ │ └── plotly-latest.min.js │ ├── tocify-1.9.1 │ │ ├── jquery.tocify.css │ │ └── jquery.tocify.js │ └── 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