Package index

Integration

Multi-level integration functions

AggregateDataByBatch.SingleCellExperiment() AggregateDataByBatch(<SingleCellExperiment>)

Aggregates feature expression by cell clusters, per batch if provided.

RunParallelDivisiveICP.SingleCellExperiment() RunParallelDivisiveICP(<SingleCellExperiment>)

Multi-level integration

Reference-mapping

Reference-mapping function

ReferenceMapping.SingleCellExperiment() ReferenceMapping(<SingleCellExperiment>,<SingleCellExperiment>)

Reference mapping

Cell state

Cell state functions

GetCellClusterProbability.SingleCellExperiment() GetCellClusterProbability(<SingleCellExperiment>)

Get ICP cell cluster probability

SummariseCellClusterProbability.SingleCellExperiment() SummariseCellClusterProbability(<SingleCellExperiment>)

Summarise ICP cell cluster probability

CellClusterProbabilityDistribution.SingleCellExperiment() CellClusterProbabilityDistribution(<SingleCellExperiment>)

Cell cluster probability distribution

BinCellClusterProbability.SingleCellExperiment() BinCellClusterProbability(<SingleCellExperiment>)

Bin cell cluster probability

TabulateCellBinsByGroup.SingleCellExperiment() TabulateCellBinsByGroup(<SingleCellExperiment>)

Tabulate cell bins by group

CellBinsFeatureCorrelation.SingleCellExperiment() CellBinsFeatureCorrelation(<SingleCellExperiment>)

Cell bins feature correlation

Cluster markers

Cluster markers functions

FindClusterMarkers.SingleCellExperiment() FindClusterMarkers(<SingleCellExperiment>)

Differential expression between cell clusters

FindAllClusterMarkers.SingleCellExperiment() FindAllClusterMarkers(<SingleCellExperiment>)

Identification of feature markers for all clusters

MajorityVotingFeatures.SingleCellExperiment() MajorityVotingFeatures(<SingleCellExperiment>)

Majority voting features by label

Dimensional reduction

Dimensional reduction functions

RunPCA.SingleCellExperiment() RunPCA(<SingleCellExperiment>)

Principal Component Analysis

RunTSNE.SingleCellExperiment() RunTSNE(<SingleCellExperiment>)

Barnes-Hut implementation of t-Distributed Stochastic Neighbor Embedding (t-SNE)

RunUMAP.SingleCellExperiment() RunUMAP(<SingleCellExperiment>)

Uniform Manifold Approximation and Projection (UMAP)

Visualization

Visualization functions

PCAElbowPlot.SingleCellExperiment() PCAElbowPlot(<SingleCellExperiment>)

Elbow plot of the standard deviations of the principal components

PlotDimRed.SingleCellExperiment() PlotDimRed(<SingleCellExperiment>)

Plot dimensional reduction categorical variables

PlotExpression.SingleCellExperiment() PlotExpression(<SingleCellExperiment>)

Plot dimensional reduction feature expression

PlotClusterTree.SingleCellExperiment() PlotClusterTree(<SingleCellExperiment>)

Plot cluster tree

VlnPlot.SingleCellExperiment() VlnPlot(<SingleCellExperiment>)

Visualization of feature expression using violin plots

HeatmapFeatures.SingleCellExperiment() HeatmapFeatures(<SingleCellExperiment>)

Heatmap visualization of the expression of features by clusters

Miscelllaneous

Miscelllaneous functions

PrepareData.SingleCellExperiment() PrepareData(<SingleCellExperiment>)

Prepare SingleCellExperiment object for analysis

GetFeatureCoefficients.SingleCellExperiment() GetFeatureCoefficients(<SingleCellExperiment>)

Get feature coefficients