├── .Rbuildignore ├── .github └── ISSUE_TEMPLATE │ ├── bug_report.md │ └── question.md ├── .gitignore ├── DESCRIPTION ├── LICENSE ├── NAMESPACE ├── NEWS ├── R ├── add_cellAnnotation.R ├── aux_export2loom.R ├── aux_exportsForArboreto.R ├── aux_geneFiltering.R ├── aux_importsFromPython.R ├── aux_regulons.R ├── aux_rss.R ├── aux_viewMotifs.R ├── class_ScenicOptions.R ├── data_exports.R ├── dotHeatmap.R ├── plotTsne_AUCellApp.R ├── plotTsne_AUCellHtml.R ├── plotTsne_compareSettings.R ├── plotTsne_rgb.R ├── priv_openDev.R ├── runCorrelation.R ├── runGenie3.R ├── runSCENIC_1_coexNetwork2modules.R ├── runSCENIC_2_createRegulons.R ├── runSCENIC_2_createRegulons_Original.R ├── runSCENIC_3_scoreCells.R ├── runSCENIC_4.R └── tsneAUC.R ├── README.md ├── Tutorials_JupyterNotebooks ├── SCENIC.png ├── SCENIC_tutorial_1-RunningVSN.html ├── SCENIC_tutorial_1-RunningVSN.ipynb ├── SCENIC_tutorial_2-ExploringOutput.html └── SCENIC_tutorial_2-ExploringOutput.ipynb ├── data └── defaultDbNames.RData ├── inst ├── CITATION ├── doc │ ├── SCENIC_Running.html │ ├── SCENIC_Setup.html │ ├── detailedStep_0_geneFilter.html │ ├── detailedStep_1_coexNetwork2modules.html │ ├── detailedStep_2_createRegulons.html │ ├── detailedStep_3_scoreCells.html │ ├── detailedStep_4_aucell_binarize.html │ └── importing_pySCENIC.html └── examples │ ├── SCENIC.loom │ └── mouseBrain_toy.loom ├── man ├── ScenicOptions-class.Rd ├── add_cell_annotation.Rd ├── calcRSS.Rd ├── defaultDbNames.Rd ├── dotHeatmap.Rd ├── export2loom.Rd ├── exportsForArboreto.Rd ├── geneFiltering.Rd ├── getDbAnnotations.Rd ├── getDbTfs.Rd ├── getRegulonName.Rd ├── getTF.Rd ├── importAUCfromText.Rd ├── importArboreto.Rd ├── importModulesGmt.Rd ├── onlyNonDuplicatedExtended.Rd ├── plotEmb_rgb.Rd ├── plotRSS.Rd ├── plotTsne_AUCellApp.Rd ├── plotTsne_AUCellHtml.Rd ├── plotTsne_compareSettings.Rd ├── regulon_plotExpression.Rd ├── regulonsToGeneLists.Rd ├── runCorrelation.Rd ├── runGenie3.Rd ├── runSCENIC_1_coexNetwork2modules.Rd ├── runSCENIC_2_createRegulons.Rd ├── runSCENIC_3_scoreCells.Rd ├── runSCENIC_4_aucell_binarize.Rd ├── selectRegulons.Rd ├── tsneAUC.Rd └── viewMotifs.Rd └── vignettes ├── FAQ.md ├── SCENIC_Running.Rmd ├── SCENIC_Setup.Rmd ├── cell.csl ├── corrected.css ├── detailedStep_0_geneFilter.Rmd ├── detailedStep_1_coexNetwork2modules.Rmd ├── detailedStep_2_createRegulons.Rmd ├── detailedStep_3_scoreCells.Rmd ├── detailedStep_4_aucell_binarize.Rmd ├── importing_pySCENIC.Rmd └── references.bib /.Rbuildignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aertslab/SCENIC/HEAD/.Rbuildignore -------------------------------------------------------------------------------- /.github/ISSUE_TEMPLATE/bug_report.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aertslab/SCENIC/HEAD/.github/ISSUE_TEMPLATE/bug_report.md 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