Installation | Introduction | Visualization | Images | Labels | Points | Shapes | Layering | Scalebars | Session info

Installation | Load SpatialData (.zarr) from Archives | Session info

Load packages | Introduction | What is DS analysis? | Starting point | Getting started | Data description | Loading the data | Preprocessing | Data preparation | Data overview | Cluster-sample sizes | Dimension reduction | Differential State (DS) analysis | Aggregation of single-cell to pseudobulk data | Pseudobulk-level MDS plot | Sample-level analysis: Pseudobulk methods | Cell-level analysis: Mixed models | Handling results | Results filtering & overview | Calculating expression frequencies | Formatting results | Visualizing results | Between-cluster concordance | DR colored by expression | Cell-level viz.: Violin plots | Sample-level viz.: Pseudobulk heatmaps | Session info | References

Load packages | Data description | Simulation framework | prepSim: Preparing data for simulation | simData: Simulating complex designs | p_dd: Simulating differential distributions | rel_lfc: Simulating cluster-specific state changes | normalize & run dimension reduction | plotting | arrangement | Simulation a hierarchical cluster structure | p_type: Introducing type features | extract gene metadata & number of clusters | filter for type genes with high expression mean | sample 100 cells per cluster for plotting | filter for type & shared genes with high expression mean | Method benchmarking | Session info | References

Load packages | Introduction | Setup | Aggregation | Analysis | Handling and visualizing results | Stagewise anaysis | Comparison | Session info | References

Preamble | Installation | Introduction | Representation | Handling | Accession | Subsetting | Internals | Annotations | Transformations | Utilities | Cropping | Masking | Querying | Combining | Coordinates | Appendix | Resources | Session info | References

Load packages | Methods | Creation of the evidence bins | P-value adjustment | Example usage | Generating input data | Differential State (DS) analysis | Generating fake bulk data | bbhw | Session info | References

Data examples | Data organization | Normalization | Normalization workflow | normCytof: Normalization using bead standards | Debarcoding | Debarcoding workflow | assignPrelim: Assignment of preliminary IDs | estCutoffs: Estimation of separation cutoffs | plotYields: Selecting barcode separation cutoffs | applyCutoffs: Applying deconvolution parameters | plotEvents: Normalized intensities | plotMahal: All barcode biaxial plot | Compensation | Compensation workflow | computeSpillmat: Estimation of the spillover matrix | plotSpillmat: Spillover matrix heatmap | compCytof: Compensation of mass cytometry data | Scatter plot visualization | Example 1: Coloring by cell density | Example 2: Coloring by variables | Example 3: Facetting by variables | Conversion to other data structures | Writing FCS files | Gating & visualization | Session information | References

Example data | Data preparation | Clustering | cluster: FlowSOM clustering & ConsensusClusterPlus metaclustering | mergeClusters: Manual cluster merging | Delta area plot | Visualization | plotCounts: Number of cells measured per sample | pbMDS: Pseudobulk-level MDS plot | Ex. 2: MDS on sample-level pseudobulks | Ex. 1: MDS on pseudobulks by cluster-sample | clrDR: Reduced dimension plot on CLR of proportions | Ex. 1: CLR on cluster proportions across samples | Ex. 2: CLR on sample proportions across clusters | plotExprHeatmap: Heatmap of aggregated marker expressions | plotPbExprs: Pseudobulk expression boxplot | plotClusterExprs: Marker-densities by cluster | plotAbundances: Relative population abundances | plotFreqHeatmap: Heatmap of cluster fequencies | plotMultiHeatmap: Multi-panel Heatmaps | Ex. 1: Type- & state-markers | Ex. 2: CDx markers & cluster frequencies | Ex. 3: Selected markers | Dimensionality reduction | Filtering | Differental testing with r BiocStyle::Biocpkg("diffcyt") | plotDiffHeatmap: Heatmap of differential testing results | Ex. 1: DA testing results | Ex. 2: DS testing results | Ex. 3: Filtering results | Ex. 4: Customizing appearance | More | Exporting FCS files | Using other clustering algorithms | Customizing visualizations | Modifying ggplots | Modifying ComplexHeatmaps | Combining ComplexHeatmaps | Ex. 1: type- & state-markers + cluster frequencies | Ex. 2: frequencies + selected markers + all markers | Session information | References

Available datasets | Loading the data | Data representation | Session information

Overview | Available datasets | Loading the data | Via accessor functions | Via ExperimentHub | Using query | Using list/loadResources | Exploring the data | Session info | References