├── .Rbuildignore ├── .gitattributes ├── .gitignore ├── DESCRIPTION ├── LICENSE ├── LICENSE.md ├── NAMESPACE ├── R ├── M1_functions.R ├── M23_functions.R ├── PAGA_functions.R ├── analysis_functions.R ├── annotation_functions.R ├── da_functions.R ├── datasets.R ├── flex_functions.R ├── hg_functions.R ├── integration_functions.R ├── marker_functions.R ├── module_functions.R ├── network_functions.R ├── plot_functions.R ├── preparation_functions.R ├── utility_functions.R └── wnn_functions.R ├── README.md ├── _pkgdown.yml ├── data ├── LR.db.rda ├── baderPathways.rda ├── cell_markers_DEG.csv ├── cell_markers_DEG.rds └── geneSets.rda ├── index.md ├── man ├── AddSModuleScore.Rd ├── LR.db.Rd ├── QC.scatterPlot.Rd ├── QC.violinPlot.Rd ├── SSNConnectivity.Rd ├── SSNExpression.Rd ├── SSNResolution.Rd ├── addLogEntry.Rd ├── aggGroupExpression.Rd ├── annotationCloud.Rd ├── autoPointSize.Rd ├── avgGroupExpression.Rd ├── baderPathways.Rd ├── balanceMatrixSize.Rd ├── balanceSamples.Rd ├── barcodeLabels.Rd ├── benchmarkCluster.Rd ├── benchmarkScores.Rd ├── categoricalColPal.Rd ├── checkGeneRep.Rd ├── citationCheck.Rd ├── cleanCluster.Rd ├── cleanFilterGenes.Rd ├── clearGlobalEnv.Rd ├── cluster.UMAP.Rd ├── clusterFilter.Rd ├── coherentFraction.Rd ├── col2rowname.Rd ├── consolidateNMF.Rd ├── da_DEG.Rd ├── da_Run.Rd ├── detectSpecies.Rd ├── dist2hclust.Rd ├── downsampleSeurat.Rd ├── eigengene.Rd ├── ens2sym.so.Rd ├── entrez2sym.Rd ├── exprUMAP.Rd ├── expression.Plot.Rd ├── featureGradient.Rd ├── filterSeurat.Rd ├── findArtifactGenes.Rd ├── findCDIMarkers.Rd ├── findConservedCDIMarkers.Rd ├── findCorMarkers.Rd ├── findGiniMarkers.Rd ├── findNetworkFeatures.Rd ├── firstup.Rd ├── fixBarcodeLabel.Rd ├── flex.asDT.Rd ├── flex.multiTabLogs.Rd ├── flex.multiTabPlot.Rd ├── flex.multiTabPlotly.Rd ├── flex.multiTabTables.Rd ├── geneRepCurve.Rd ├── geneSets.Rd ├── geom_split_violin.Rd ├── getAnnotationPathways.Rd ├── getClusterCenters.Rd ├── getConnectivity.Rd ├── getDEG.Rd ├── getDensity.Rd ├── getExpressedGenes.Rd ├── getExpressingCells.Rd ├── getExpressionMatrix.Rd ├── getICAGenes.Rd ├── getJaccard.Rd ├── getLoadPath.Rd ├── getMitoContent.Rd ├── getModuleGenes.Rd ├── getModulePreservation.Rd ├── getNMFGenes.Rd ├── getNodesEdges.Rd ├── getOrderedGroups.Rd ├── getReductionGenes.Rd ├── getSoftThreshold.Rd ├── getSoftThreshold2.Rd ├── getUMAP.Rd ├── group2list.Rd ├── highlightUMAP.Rd ├── id2geneset.Rd ├── id2term.Rd ├── inferSpecies.Rd ├── inferState.Rd ├── initiateLog.Rd ├── jaccardSimilarityMatrix.Rd ├── lintersect.Rd ├── loadCellRanger.Rd ├── loadMat.Rd ├── loadMoffat.Rd ├── longDF2namedList.Rd ├── mergeSeuratList.Rd ├── mikoScore.Rd ├── miko_heatmap.Rd ├── miko_integrate.Rd ├── miko_message.Rd ├── miko_volcano.Rd ├── multiCluster.Rd ├── multiSilhouette.Rd ├── multiSpecificity.Rd ├── namedList2longDF.Rd ├── namedList2wideDF.Rd ├── neighborPurity.Rd ├── netHG.Rd ├── nullScore.Rd ├── optimalBinSize.Rd ├── optimalDS.Rd ├── orderedFactor.Rd ├── p2z.Rd ├── parCor.Rd ├── pcaElbow.Rd ├── prepGeneList.Rd ├── prepSeurat.Rd ├── prepSeurat2.Rd ├── projectReduction.Rd ├── propVarPCA.Rd ├── pruneSSN.Rd ├── pseudoReplicates.Rd ├── pseudotimeRF.Rd ├── qNorm.Rd ├── recodeBarcode.Rd ├── rescaleValues.Rd ├── rmDuplicateGenes.Rd ├── rmvCSVprefix.Rd ├── runAUC.Rd ├── runAUGUR.Rd ├── runBBKNN.Rd ├── runGSEA.Rd ├── runHG.Rd ├── runICA.Rd ├── runMS.Rd ├── runNMF.Rd ├── runRPCA.Rd ├── runSSN.Rd ├── runScanorama.Rd ├── runWGCNA.Rd ├── saveHTML.Rd ├── savePDF.Rd ├── scExpression.UMAP.Rd ├── scMikoUpdate.Rd ├── scNormScale.Rd ├── scaleFreeNet.Rd ├── scaleTOM.Rd ├── scale_color_miko.Rd ├── scale_fill_miko.Rd ├── scoreGBM.Rd ├── scoreStem.Rd ├── searchAnnotations.Rd ├── setResolution.Rd ├── sigScore.Rd ├── signatureCoherence.Rd ├── sim2adj.Rd ├── snip.Rd ├── sparse2dense.Rd ├── sparse2df.Rd ├── speciesConvert.Rd ├── springNet.Rd ├── subsetDimRed.Rd ├── subsetSeurat.Rd ├── summarizeHG.Rd ├── summarizeModules.Rd ├── sym2ens.Rd ├── sym2entrez.Rd ├── term2id.Rd ├── theme_miko.Rd ├── ulength.Rd ├── uniqueFeatures.Rd ├── updateCentralLog.Rd ├── updateDimNames.Rd ├── updateGeneSets.Rd ├── upset.Plot.Rd ├── value2col.Rd ├── varExpPCA.Rd ├── variableGenes.Plot.Rd ├── vd_Formula.Rd ├── vd_Inputs.Rd ├── vd_Run.Rd ├── vd_UMAP.Rd ├── wgcna2graphDF.Rd ├── wideDF2namedList.Rd ├── wnn_Components.Rd ├── wnn_Run.Rd └── z2p.Rd ├── scMiko.Rproj └── vignettes ├── Cell_Annotation.Rmd ├── Cluster_Optimization.Rmd ├── DEG.Rmd ├── Marker_Catalog.Rmd ├── Module_Detection.Rmd ├── assets ├── atlas_cao2019.png ├── atlas_cao2020.png ├── atlas_mannos2021.png ├── atlas_ps2019.png ├── atlas_tm.png ├── atlas_ts.png ├── atlas_tyser2021.png └── atlas_zeisel2018.png ├── install.Rmd ├── scPipeline_analysis_workflows.Rmd ├── scPipeline_getting_started.Rmd └── scPipeline_module_overview.Rmd /.Rbuildignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NMikolajewicz/scMiko/HEAD/.Rbuildignore 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