Man pages for edroaldo/fusca
Framework for Unified Single-Cell Analysis
| activeSignaling | Create gene regulator subnetworks based on gene signature... |
| AddAssay | Add assay |
| addInfo | Add metadata information to CellRouter object. |
| apply1_sp | Apply for sparse matrix. |
| apply2_sp | Apply for sparse matrix. |
| buildGRN2-methods | Predict a gene regulatory network. |
| buildGRN-methods | Predict a gene regulatory network. |
| buildKNN-methods | Build kNN graph. |
| calculateCentroids-methods | Calculate cluster centroids |
| calculateDistanceMatrix-methods | Calculate distance matrix |
| calculateLigandReceptor | Calculate Ligand and Receptors |
| calculateObservedMean | Mean expression between ligands and receptors. |
| calculatePvalue | Calculate the p-value for the interactions. |
| CellComm | The CellComm class. |
| cellnetwork3 | Calculate cell network based on number of interactions in the... |
| cellnetworksPPI | Create a weighted protein-protein interaction network based... |
| cellnetworksPPI2 | Create a weighted protein-protein interaction network based... |
| CellRouter | The CellRouter class. |
| center_with_threshold | Center the data using threshold. |
| clustergenes | Helper function of clusterGenesPseudotime. |
| clusterGenesPseudotime-methods | Cluster kinetic profiles along trajectories. |
| clusterPermutation | Performs cluster/cell type permutations to estimate an... |
| clusterPermutationSubcluster | Performs cluster/cell type permutations to estimate an... |
| cn_sampR_to_pattern | Helper function of ranked_findSpecGenes. |
| cn_testPattern | Helper function of ranked_findSpecGenes. |
| commToNames | Assign names to subpopulations. |
| compareTwoGroups-methods | Compute fold changes and find gene signatures. |
| computeDC | Dimensionality reduction using diffusion components. |
| computeFC-methods | Compute fold changes and find gene signatures. |
| computePCA-methods | Perform principal component analysis. |
| computeTSNE-methods | Perform t-SNE. |
| computeUMAP-methods | Perform UMAP. |
| computeValue-methods | Compute expression statistics of each gene in each... |
| computeValueSubclusters-methods | Compute expression statistics of each gene in each... |
| convertID | Helper function of convertIDs. |
| convertIDs | Helper function of pathwayenrichment. |
| correlationPseudotime-methods | Compute the correlation of each gene along the trajectories. |
| cRamp | Convert x to 4 rainbow colors. |
| cRamp2 | Convert to values to 'white', "goldenrod1", and "darkorange2"... |
| cRampClust | Convert values to colors. |
| CreateCellComm | Create CellComm object. |
| CreateCellRouter | Create CellRouter. |
| createNetworksFromPaths | Create networks from paths. |
| createPaths | Create paths. |
| createPPI | Create protein-protein interactions. |
| createTFNetwork | Create transcription factor network. |
| curves_info | Helper function of processCurves. |
| customSpace-methods | Customized coordinates used to visualize data in a reduced... |
| dotplotByMetadata-methods | Dot plot of genes in populations. |
| dotplot-methods | Dot plot of genes in populations. |
| dotplotSignatureScore-methods | Dot plot signature score. |
| extractRegulators | Extract transcriptional regulators. |
| filterCells | Quality control. |
| findClusters-methods | Identify clusters. |
| find_curve | Find curve |
| findCurves-methods | Find pseudo-time curves. |
| findmarkers | Helper function of findSignatures. |
| findPaths-methods | Identify trajectories connecting source and target... |
| findPathsRJava-methods | Identify trajectories connecting source and target... |
| findpaths.simple-methods | Identify trajectories connecting populations in the... |
| findpaths.simpleRJava-methods | Identify signaling pathways connecting cell surface receptors... |
| find_sequence | Find population sequence |
| findSignatures | Identify gene signatures. |
| findSubclusters-methods | Find subclusters |
| find_tfs | Find transcription factors. |
| FindVariableGenes | Find Variable Genes |
| FuscaAssay-class | CellRouter assay. |
| getIndexes | Create heatmaps with gene signatures. |
| globalGRN | Create global gene regulatory network. |
| graphClustering-methods | Graph-based clustering. |
| grnScoresHeatmap-methods | Compute and plot heatmap of GRN scores for transcriptional... |
| grnscores-methods | Compute and plot GRN scores for transcriptional regulators. |
| ig_tabToIgraph | Create an igraph object for the gene regulatory network. |
| interactionmatrix | Compute the cell-cell interaction data frame. |
| mat_zscores | GRN reconstruction. |
| modelClustering | Model-based clustering using the Mclust package. |
| multiplot | Combine multiple plots into a single one. |
| nodeLabels | Assign labels for subpopulations. |
| Normalize-methods | Normalize the data. |
| pathsinfo | Helper function of processTrajectories. |
| pathwaycluster-methods | Plot pathway enrichment analysis heatmap. |
| pathwayenrichment-methods | Pathway enrichment analysis |
| pipe | Pipe operator |
| plotbranch-methods | Plot branch-specific kinetic patterns. |
| plotClusterHeatmap-methods | Plot cluster heatmap. |
| plotClusterProfiler | Plot pathway enrichment analysis results. |
| plotClusters-methods | Plot kinetic trends for genes in transcriptional clusters. |
| plotDRExpression2-methods | Show gene expression in the space of reduced dimensionality. |
| plotDRExpression-methods | Show gene expression in the space of reduced dimensionality. |
| plotEnrichR | Plot Enrichment Result |
| plotGenesInClusters-methods | Plot top-ranked genes in transcriptional clusters. |
| plotIntegration | Plot spatial clusters |
| plotInteractionMatrix2 | Plot inferred cell-cell interaction network. |
| plotInteractionNetwork | Plot graph of interactions. |
| plotKNN-methods | Plot kNN graph. |
| plotPairDotplot | Plot pair dotplot. |
| plotPathHeatmap-methods | Plot path heatmap. |
| plotpaths-methods | Plot information about genes in selected paths. |
| plotProportion | Proportion plot. |
| plotProportion2 | Proportion plot. |
| plotReducedDimension | Plot reduced dimension space. |
| plotRegulonDynamics-methods | Plot regulon dynamics. |
| plotSelectedClusters | Plot selected spatial clusters |
| plotSignaturesBoxplot | Plot boxplot with gene signatures. |
| plotSignatureScoreDynamics-methods | Plot signature scores along a trajectory. |
| plotSignatureScore-methods | Show gene expression in the space of reduced dimensionality. |
| plotSignaturesHeatmap | Plot heatmap with gene signatures. |
| plotSpatialClusters | Plot spatial clusters |
| plotSpatialExpression | Plot spatial expression |
| plotSpatialScore-methods | Plot spatial expression |
| plotSpatialSubclusters | Plot subclusters |
| plottrajectories-methods | Plot genes along specified trajectories. |
| plottrajectory-methods | Plot genes along a trajectory. |
| plottr-methods | Plot derivative and kinetic patterns of predicted regulators. |
| plotValue-methods | Show any numeric value in the CellRouter metadata table in... |
| plotViolin | Plot violin plot. |
| population.pairing | Compute cell-cell interaction network. |
| predictCellCycle | Predict cell cycle phase. |
| predictCellInteractions | Predict Cell Interactions |
| predictState | Predict state based on scored gene lists. |
| processCurves-methods | Process curves |
| processTrajectories-methods | Process trajectories. |
| range01 | Rescale x from 0 to 1. |
| ranked_findSpecGenes | Helper function of findSignatures. |
| rankGenesTranscriptionalClusters-methods | Rank genes in transcriptional clusters. |
| rankpaths | Rank signaling pathways. |
| read10X | Read 10X expression data. |
| read10XImage-methods | Read ST metadata. |
| regulatornetwork | Plot subnetworks for selected transcriptional regulators in... |
| scaleData-methods | Scale data |
| scale.sparse | Scale sparse matrix dividing it in blocks. |
| scoreGeneSets | Score gene sets. |
| signaling2TF | Signaling to transcription factors. |
| smoothDynamics-methods | Smooth dynamics along trajectories. |
| sourcestargets | Create source target list for each interaction. |
| sparse.cor | Correlation function for sparse matrix. |
| sparse.cor2 | Correlation function for sparse matrix. |
| stat_bag | Helper function of plotReducedDimension. |
| StatBag | Helper function of stat_bag. |
| summarize.flow | Summarize flow network. |
| testExport | Test |
| topGenes-methods | Find genes highly correlated with pseudotime. |
| verify_gene_exp | Verify gene expression. |
