├── .Rbuildignore ├── .github ├── .gitignore └── workflows │ └── render-rmarkdown.yaml ├── .gitignore ├── DESCRIPTION ├── LICENSE ├── LICENSE.md ├── NAMESPACE ├── NEWS.md ├── R ├── RcppExports.R ├── dimension_reduction.R ├── grn.R ├── pair_cells.R ├── peak_to_gene.R ├── select_tf_gene.R ├── trajectory_analysis.R ├── utils.R └── visualization.R ├── README.md ├── _pkgdown.yml ├── data ├── geneAnnoHg19.rda ├── geneAnnoHg38.rda ├── geneAnnoMm10.rda └── geneAnnoMm9.rda ├── docs ├── 404.html ├── LICENSE-text.html ├── LICENSE.html ├── articles │ ├── cardiomyocyte-GRN.html │ ├── index.html │ ├── install.html │ ├── myofibroblast-GRN.html │ ├── myofibroblast-GRN_files │ │ └── figure-html │ │ │ ├── unnamed-chunk-1-1.png │ │ │ ├── unnamed-chunk-10-1.png │ │ │ ├── unnamed-chunk-11-1.png │ │ │ ├── unnamed-chunk-13-1.png │ │ │ ├── unnamed-chunk-14-1.png │ │ │ ├── unnamed-chunk-16-1.png │ │ │ ├── unnamed-chunk-18-1.png │ │ │ ├── unnamed-chunk-2-1.png │ │ │ ├── unnamed-chunk-20-1.png │ │ │ ├── unnamed-chunk-21-1.png │ │ │ ├── unnamed-chunk-23-1.png │ │ │ ├── unnamed-chunk-25-1.png │ │ │ ├── unnamed-chunk-27-1.png │ │ │ ├── unnamed-chunk-28-1.png │ │ │ ├── unnamed-chunk-3-1.png │ │ │ ├── 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 │ │ │ ├── unnamed-chunk-9-1.png │ │ │ └── viz_network-1.png │ ├── pbmc_10x_multiome.html │ └── pbmc_10x_multiome_files │ │ └── figure-html │ │ ├── unnamed-chunk-11-1.png │ │ ├── unnamed-chunk-13-1.png │ │ ├── unnamed-chunk-17-1.png │ │ ├── unnamed-chunk-19-1.png │ │ ├── unnamed-chunk-20-1.png │ │ ├── unnamed-chunk-21-1.png │ │ ├── unnamed-chunk-23-1.png │ │ ├── unnamed-chunk-25-1.png │ │ ├── unnamed-chunk-26-1.png │ │ ├── unnamed-chunk-4-1.png │ │ └── unnamed-chunk-8-1.png ├── authors.html ├── bootstrap-toc.css ├── bootstrap-toc.js ├── docsearch.css ├── docsearch.js ├── index.html ├── link.svg ├── news │ └── index.html ├── pkgdown.css ├── pkgdown.js ├── pkgdown.yml ├── reference │ ├── AddTargetAssay.html │ ├── AddTrajectory.html │ ├── CellPropPlot-1.png │ ├── CellPropPlot.html │ ├── CoembedData.html │ ├── CompareCellProp.html │ ├── CorrelationHeatmap.html │ ├── CorrelationPlot.html │ ├── CreatePairedObject.html │ ├── GRNHeatmap.html │ ├── GRNPlot.html │ ├── GRNSpatialPlot.html │ ├── GetCorrelation.html │ ├── GetGRN.html │ ├── GetPairList.html │ ├── GetTFGeneCorrelation.html │ ├── GetTrajectory.html │ ├── NetCentPlot.html │ ├── PairCells.html │ ├── PeakToGene.html │ ├── PseudotimePlot.html │ ├── Rplot001.png │ ├── RunDiffusionMap.html │ ├── SelectGenes.html │ ├── SelectTFs.html │ ├── TopEmbGRN.html │ ├── TrajectoryHeatmap.html │ ├── TrajectoryPlot.html │ ├── figures │ │ └── schematic.png │ └── index.html └── sitemap.xml ├── man ├── AddTargetAssay.Rd ├── AddTrajectory.Rd ├── CellPropPlot.Rd ├── CoembedData.Rd ├── CompareCellProp.Rd ├── CorrelationHeatmap.Rd ├── CorrelationPlot.Rd ├── CreatePairedObject.Rd ├── GRNHeatmap.Rd ├── GRNPlot.Rd ├── GRNSpatialPlot.Rd ├── GetCorrelation.Rd ├── GetGRN.Rd ├── GetPairList.Rd ├── GetTFGeneCorrelation.Rd ├── GetTrajectory.Rd ├── NetCentPlot.Rd ├── PairCells.Rd ├── PeakToGene.Rd ├── PseudotimePlot.Rd ├── RunDiffusionMap.Rd ├── SelectGenes.Rd ├── SelectTFs.Rd ├── TopEmbGRN.Rd ├── TrajectoryHeatmap.Rd ├── TrajectoryPlot.Rd └── figures │ ├── .DS_Store │ └── schematic.png ├── pkgdown └── index.md ├── run.sh ├── scMEGA.Rproj ├── src ├── .gitignore ├── Correlation.cpp └── RcppExports.cpp └── vignettes ├── .gitignore ├── cardiomyocyte-GRN.Rmd ├── install.Rmd ├── myofibroblast-GRN.Rmd └── pbmc_10x_multiome.Rmd /.Rbuildignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CostaLab/scMEGA/HEAD/.Rbuildignore -------------------------------------------------------------------------------- /.github/.gitignore: -------------------------------------------------------------------------------- 1 | *.html 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