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 |