Files in edroaldo/fusca

Framework for Unified Single-Cell Analysis

R/CellComm_class.R R/CellComm_functions.R R/CellRouter_class.R R/Normalize_method.R R/activeSignaling_CellComm.R R/addInfo.R R/buildGRN_method.R R/buildKNN.R R/cRamp_helper.R R/calculateObservedMean_CellComm.R R/calculatePvalue_CellComm.R R/cellnetwork3_CellComm.R R/cellnetworksPPI_CellComm.R R/clusterGenesPseudotime_method.R R/clusterPermutation_CellComm.R R/compareTwoGroups.R R/computeDC.R R/computePCA_method.R R/computeTSNE_method.R R/computeUMAP.R R/computeValue.R R/correlationPseudotime_method.R R/createPPI_CellComm.R R/createPathsAndNetworks.R R/createTFNetwork.R R/customSpace_method.R R/dotplotSignatureScore.R R/dotplot_method.R R/filterCells.R R/findClusters.R R/findCurves_method.R R/findPathsRJava.R R/findPaths_method.R R/findSignatures.R R/findpaths.simpleRJava_CellComm.R R/findpaths.simple_CellComm.R R/grnScoresHeatmap.R R/grnscores_method.R R/helpers_sparse_matrix.R R/integration.R R/interactionmatrix_CellComm.R R/onLoad.R R/pathwaycluster.R R/pathwayenrichment.R R/plotClusterHeatmap_method.R R/plotClusterProfiler_CellComm.R R/plotClusters_method.R R/plotDRExpression_method.R R/plotEnrichR.R R/plotGenesInClusters.R R/plotInteraction_CellComm.R R/plotKNN.R R/plotPairDotplot_CellComm.R R/plotPathHeatmap_method.R R/plotProportion.R R/plotReducedDimension.R R/plotRegulonDynamics.R R/plotSignatureScore.R R/plotSignatureScoreDynamics.R R/plotSignaturesBoxplot.R R/plotSignaturesHeatmap.R R/plotValue.R R/plotViolin.R R/plot_helper_functions.R R/plotbranch_method.R R/plotpaths.R R/plottr_method.R R/plottrajectories_method.R R/population.pairing_CellComm.R R/predictCell.R R/preprocessing.R R/processCurves.R R/processTrajectories_method.R R/rankGenesTranscriptionalClusters.R R/rankpaths_CellComm.R R/regulatornetwork.R R/scoreGeneSets.R R/signaling2TF_CellComm.R R/smoothDynamics_method.R R/sourcestargets_CellComm.R R/spatial_transcriptomics.R R/subsetCells.R R/summarize.flow_CellComm.R R/topGenes_method.R R/utils-pipe.R README.md man/AddAssay.Rd man/CellComm.Rd man/CellRouter.Rd man/CreateCellComm.Rd man/CreateCellRouter.Rd man/FindVariableGenes.Rd man/FuscaAssay-class.Rd man/Normalize-methods.Rd man/StatBag.Rd man/activeSignaling.Rd man/addInfo.Rd man/apply1_sp.Rd man/apply2_sp.Rd man/buildGRN-methods.Rd man/buildGRN2-methods.Rd man/buildKNN-methods.Rd man/cRamp.Rd man/cRamp2.Rd man/cRampClust.Rd man/calculateCentroids-methods.Rd man/calculateDistanceMatrix-methods.Rd man/calculateLigandReceptor.Rd man/calculateObservedMean.Rd man/calculatePvalue.Rd man/cellnetwork3.Rd man/cellnetworksPPI.Rd man/cellnetworksPPI2.Rd man/center_with_threshold.Rd man/clusterGenesPseudotime-methods.Rd man/clusterPermutation.Rd man/clusterPermutationSubcluster.Rd man/clustergenes.Rd man/cn_sampR_to_pattern.Rd man/cn_testPattern.Rd man/commToNames.Rd man/compareTwoGroups-methods.Rd man/computeDC.Rd man/computeFC-methods.Rd man/computePCA-methods.Rd man/computeTSNE-methods.Rd man/computeUMAP-methods.Rd man/computeValue-methods.Rd man/computeValueSubclusters-methods.Rd man/convertID.Rd man/convertIDs.Rd man/correlationPseudotime-methods.Rd man/createNetworksFromPaths.Rd man/createPPI.Rd man/createPaths.Rd man/createTFNetwork.Rd man/curves_info.Rd man/customSpace-methods.Rd man/dotplot-methods.Rd man/dotplotByMetadata-methods.Rd man/dotplotSignatureScore-methods.Rd man/extractRegulators.Rd man/filterCells.Rd man/findClusters-methods.Rd man/findCurves-methods.Rd man/findPaths-methods.Rd man/findPathsRJava-methods.Rd man/findSignatures.Rd man/findSubclusters-methods.Rd man/find_curve.Rd man/find_sequence.Rd man/find_tfs.Rd man/findmarkers.Rd man/findpaths.simple-methods.Rd man/findpaths.simpleRJava-methods.Rd man/getIndexes.Rd man/globalGRN.Rd man/graphClustering-methods.Rd man/grnScoresHeatmap-methods.Rd man/grnscores-methods.Rd man/ig_tabToIgraph.Rd man/interactionmatrix.Rd man/mat_zscores.Rd man/modelClustering.Rd man/multiplot.Rd man/nodeLabels.Rd man/pathsinfo.Rd man/pathwaycluster-methods.Rd man/pathwayenrichment-methods.Rd man/pipe.Rd man/plotClusterHeatmap-methods.Rd man/plotClusterProfiler.Rd man/plotClusters-methods.Rd man/plotDRExpression-methods.Rd man/plotDRExpression2-methods.Rd man/plotEnrichR.Rd man/plotGenesInClusters-methods.Rd man/plotIntegration.Rd man/plotInteractionMatrix2.Rd man/plotInteractionNetwork.Rd man/plotKNN-methods.Rd man/plotPairDotplot.Rd man/plotPathHeatmap-methods.Rd man/plotProportion.Rd man/plotProportion2.Rd man/plotReducedDimension.Rd man/plotRegulonDynamics-methods.Rd man/plotSelectedClusters.Rd man/plotSignatureScore-methods.Rd man/plotSignatureScoreDynamics-methods.Rd man/plotSignaturesBoxplot.Rd man/plotSignaturesHeatmap.Rd man/plotSpatialClusters.Rd man/plotSpatialExpression.Rd man/plotSpatialScore-methods.Rd man/plotSpatialSubclusters.Rd man/plotValue-methods.Rd man/plotViolin.Rd man/plotbranch-methods.Rd man/plotpaths-methods.Rd man/plottr-methods.Rd man/plottrajectories-methods.Rd man/plottrajectory-methods.Rd man/population.pairing.Rd man/predictCellCycle.Rd man/predictCellInteractions.Rd man/predictState.Rd man/processCurves-methods.Rd man/processTrajectories-methods.Rd man/range01.Rd man/rankGenesTranscriptionalClusters-methods.Rd man/ranked_findSpecGenes.Rd man/rankpaths.Rd man/read10X.Rd man/read10XImage-methods.Rd man/regulatornetwork.Rd man/scale.sparse.Rd man/scaleData-methods.Rd man/scoreGeneSets.Rd man/signaling2TF.Rd man/smoothDynamics-methods.Rd man/sourcestargets.Rd man/sparse.cor.Rd man/sparse.cor2.Rd man/stat_bag.Rd man/summarize.flow.Rd man/testExport.Rd man/topGenes-methods.Rd man/verify_gene_exp.Rd tutorial/README.md