Coralysis sensitive identification of imbalanced cell types and
states in single-cell data via multi-level integration
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Documentation for package ‘Coralysis’ version 0.99.6
Help Pages
| AggregateDataByBatch | Aggregates feature expression by cell clusters, per batch if provided. |
| AggregateDataByBatch-method | Aggregates feature expression by cell clusters, per batch if provided. |
| AggregateDataByBatch.SingleCellExperiment | Aggregates feature expression by cell clusters, per batch if provided. |
| BinCellClusterProbability | Bin cell cluster probability |
| BinCellClusterProbability-method | Bin cell cluster probability |
| BinCellClusterProbability.SingleCellExperiment | Bin cell cluster probability |
| CellBinsFeatureCorrelation | Cell bins feature correlation |
| CellBinsFeatureCorrelation-method | Cell bins feature correlation |
| CellBinsFeatureCorrelation.SingleCellExperiment | Cell bins feature correlation |
| CellClusterProbabilityDistribution | Cell cluster probability distribution |
| CellClusterProbabilityDistribution-method | Cell cluster probability distribution |
| CellClusterProbabilityDistribution.SingleCellExperiment | Cell cluster probability distribution |
| FindAllClusterMarkers | Identification of feature markers for all clusters |
| FindAllClusterMarkers-method | Identification of feature markers for all clusters |
| FindAllClusterMarkers.SingleCellExperiment | Identification of feature markers for all clusters |
| FindClusterMarkers | Differential expression between cell clusters |
| FindClusterMarkers-method | Differential expression between cell clusters |
| FindClusterMarkers.SingleCellExperiment | Differential expression between cell clusters |
| GetCellClusterProbability | Get ICP cell cluster probability |
| GetCellClusterProbability-method | Get ICP cell cluster probability |
| GetCellClusterProbability.SingleCellExperiment | Get ICP cell cluster probability |
| GetFeatureCoefficients | Get feature coefficients |
| GetFeatureCoefficients-method | Get feature coefficients |
| GetFeatureCoefficients.SingleCellExperiment | Get feature coefficients |
| HeatmapFeatures | Heatmap visualization of the expression of features by clusters |
| HeatmapFeatures-method | Heatmap visualization of the expression of features by clusters |
| HeatmapFeatures.SingleCellExperiment | Heatmap visualization of the expression of features by clusters |
| MajorityVotingFeatures | Majority voting features by label |
| MajorityVotingFeatures-method | Majority voting features by label |
| MajorityVotingFeatures.SingleCellExperiment | Majority voting features by label |
| PCAElbowPlot | Elbow plot of the standard deviations of the principal components |
| PCAElbowPlot-method | Elbow plot of the standard deviations of the principal components |
| PCAElbowPlot.SingleCellExperiment | Elbow plot of the standard deviations of the principal components |
| PlotClusterTree | Plot cluster tree |
| PlotClusterTree-method | Plot cluster tree |
| PlotClusterTree.SingleCellExperiment | Plot cluster tree |
| PlotDimRed | Plot dimensional reduction categorical variables |
| PlotDimRed-method | Plot dimensional reduction categorical variables |
| PlotDimRed.SingleCellExperiment | Plot dimensional reduction categorical variables |
| PlotExpression | Plot dimensional reduction feature expression |
| PlotExpression-method | Plot dimensional reduction feature expression |
| PlotExpression.SingleCellExperiment | Plot dimensional reduction feature expression |
| PrepareData | Prepare 'SingleCellExperiment' object for analysis |
| PrepareData-method | Prepare 'SingleCellExperiment' object for analysis |
| PrepareData.SingleCellExperiment | Prepare 'SingleCellExperiment' object for analysis |
| ReferenceMapping | Reference mapping |
| ReferenceMapping-method | Reference mapping |
| ReferenceMapping.SingleCellExperiment | Reference mapping |
| RunBPParallelDivisiveICP | Multi-level integration |
| RunParallelDivisiveICP | Multi-level integration |
| RunParallelDivisiveICP-method | Multi-level integration |
| RunParallelDivisiveICP.SingleCellExperiment | Multi-level integration |
| RunPCA | Principal Component Analysis |
| RunPCA-method | Principal Component Analysis |
| RunPCA.SingleCellExperiment | Principal Component Analysis |
| RunTSNE | Barnes-Hut implementation of t-Distributed Stochastic Neighbor Embedding (t-SNE) |
| RunTSNE-method | Barnes-Hut implementation of t-Distributed Stochastic Neighbor Embedding (t-SNE) |
| RunTSNE.SingleCellExperiment | Barnes-Hut implementation of t-Distributed Stochastic Neighbor Embedding (t-SNE) |
| RunUMAP | Uniform Manifold Approximation and Projection (UMAP) |
| RunUMAP-method | Uniform Manifold Approximation and Projection (UMAP) |
| RunUMAP.SingleCellExperiment | Uniform Manifold Approximation and Projection (UMAP) |
| SummariseCellClusterProbability | Summarise ICP cell cluster probability |
| SummariseCellClusterProbability-method | Summarise ICP cell cluster probability |
| SummariseCellClusterProbability.SingleCellExperiment | Summarise ICP cell cluster probability |
| TabulateCellBinsByGroup | Tabulate cell bins by group |
| TabulateCellBinsByGroup-method | Tabulate cell bins by group |
| TabulateCellBinsByGroup.SingleCellExperiment | Tabulate cell bins by group |
| VlnPlot | Visualization of feature expression using violin plots |
| VlnPlot-method | Visualization of feature expression using violin plots |
| VlnPlot.SingleCellExperiment | Visualization of feature expression using violin plots |