├── .DS_Store ├── .Rbuildignore ├── .gitignore ├── Big_Connectome.png ├── DESCRIPTION ├── LICENSE ├── NAMESPACE ├── R ├── .DS_Store ├── CellCellScatter.r ├── Centrality.R ├── CircosDiff.R ├── CircosPlot.R ├── CompareCentrality.R ├── CreateConnectome.r ├── DOR.R ├── DiffEdgeDotPlot.R ├── DifferentialConnectome.R ├── DifferentialScoringPlot.R ├── EdgeDotPlot.R ├── EvenSplit.R ├── FilterConnectome.R ├── ModalDotPlot.r ├── NetworkPlot.r ├── PercentExpression_v2.R ├── SignalScatter.r ├── SignalingTSNE.R ├── SingleCellConnectome.R └── SplitMarkers.R ├── README.md ├── _pkgdown.yml ├── connectome.Rproj ├── data ├── .DS_Store ├── ncomms8866_human.rda ├── ncomms8866_mouse.rda ├── ncomms8866_orig.rda ├── ncomms8866_pig.rda ├── ncomms8866_rat.rda └── translator.rda ├── docs ├── 404.html ├── articles │ ├── 01 Connectome Workflow.html │ ├── 01 Connectome Workflow_files │ │ └── figure-html │ │ │ ├── unnamed-chunk-10-1.png │ │ │ ├── unnamed-chunk-11-1.png │ │ │ ├── unnamed-chunk-14-1.png │ │ │ ├── unnamed-chunk-14-2.png │ │ │ ├── unnamed-chunk-14-3.png │ │ │ ├── unnamed-chunk-14-4.png │ │ │ ├── unnamed-chunk-15-1.png │ │ │ ├── unnamed-chunk-16-1.png │ │ │ ├── unnamed-chunk-17-1.png │ │ │ ├── unnamed-chunk-4-1.png │ │ │ ├── unnamed-chunk-6-1.png │ │ │ ├── unnamed-chunk-6-2.png │ │ │ ├── unnamed-chunk-7-1.png │ │ │ ├── unnamed-chunk-8-1.png │ │ │ └── unnamed-chunk-9-1.png │ ├── 02 Differential Connectomics.html │ ├── 02 Differential Connectomics_files │ │ └── figure-html │ │ │ ├── unnamed-chunk-10-1.png │ │ │ ├── unnamed-chunk-11-1.png │ │ │ ├── unnamed-chunk-12-1.png │ │ │ ├── unnamed-chunk-13-1.png │ │ │ ├── unnamed-chunk-5-1.png │ │ │ ├── unnamed-chunk-6-1.png │ │ │ ├── unnamed-chunk-7-1.png │ │ │ ├── unnamed-chunk-8-1.png │ │ │ └── unnamed-chunk-9-1.png │ ├── 03 Centrality Plots.html │ ├── 03 Centrality Plots_files │ │ └── figure-html │ │ │ ├── unnamed-chunk-4-1.png │ │ │ ├── unnamed-chunk-5-1.png │ │ │ ├── unnamed-chunk-6-1.png │ │ │ ├── unnamed-chunk-7-1.png │ │ │ └── unnamed-chunk-8-1.png │ ├── 04 Comparative and Longitudinal Connectomics.html │ ├── 04 Comparative and Longitudinal Connectomics_files │ │ └── figure-html │ │ │ ├── unnamed-chunk-5-1.png │ │ │ ├── unnamed-chunk-6-1.png │ │ │ ├── unnamed-chunk-7-1.png │ │ │ └── unnamed-chunk-9-1.png │ └── index.html ├── authors.html ├── bootstrap-toc.css ├── bootstrap-toc.js ├── docsearch.css ├── docsearch.js ├── index.html ├── link.svg ├── pkgdown.css ├── pkgdown.js ├── pkgdown.yml └── reference │ ├── CellCellScatter.html │ ├── Centrality.html │ ├── CircosDiff.html │ ├── CircosPlot.html │ ├── CompareCentrality.html │ ├── CreateConnectome.html │ ├── DOR.html │ ├── DifferentialConnectome.html │ ├── DifferentialScoringPlot.html │ ├── FilterConnectome.html │ ├── ModalDotPlot.html │ ├── NetworkPlot.html │ ├── SignalScatter.html │ ├── SignalingTSNE.html │ ├── figures │ └── Big_Connectome.png │ └── index.html ├── man ├── CellCellScatter.Rd ├── Centrality.Rd ├── CircosDiff.Rd ├── CircosPlot.Rd ├── 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