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| adaptSpillmat | Adapt spillover matrix |
| applyCutoffs | Single-cell debarcoding (2) |
| assignPrelim | Single-cell debarcoding (1) |
| channels | 'SingleCellExperiment' accessors |
| channels-method | 'SingleCellExperiment' accessors |
| clrDR | DR plot on CLR of proportions |
| cluster | 'FlowSOM' clustering & 'ConsensusClusterPlus' metaclustering |
| cluster_codes | 'SingleCellExperiment' accessors |
| cluster_codes-method | 'SingleCellExperiment' accessors |
| cluster_ids | 'SingleCellExperiment' accessors |
| cluster_ids-method | 'SingleCellExperiment' accessors |
| compCytof | Compensate CyTOF data |
| computeSpillmat | Compute spillover matrix |
| data | Example data sets |
| delta_area | 'SingleCellExperiment' accessors |
| delta_area-method | 'SingleCellExperiment' accessors |
| ei | 'SingleCellExperiment' accessors |
| ei-method | 'SingleCellExperiment' accessors |
| estCutoffs | Estimation of distance separation cutoffs |
| extractClusters | Extract clusters from a 'SingleCellExperiment' |
| filterSCE | 'SingleCellExperiment' filtering |
| guessPanel | Guess parameter panel |
| isotope_list | Example data sets |
| marker_classes | 'SingleCellExperiment' accessors |
| marker_classes-method | 'SingleCellExperiment' accessors |
| mergeClusters | Manual cluster merging |
| merging_table | Example data sets |
| mp_cells | Example data sets |
| normCytof | Bead-based normalization |
| n_cells | 'SingleCellExperiment' accessors |
| n_cells-method | 'SingleCellExperiment' accessors |
| PBMC_fs | Example data sets |
| PBMC_md | Example data sets |
| PBMC_panel | Example data sets |
| pbMDS | Pseudobulk-level MDS plot |
| plotAbundances | Population frequencies across samples & clusters |
| plotClusterExprs | Plot expression distributions by cluster |
| plotClusterHeatmap | Plot cluster heatmap |
| plotCodes | tSNE and PCA on SOM codes |
| plotCounts | Plot cell counts |
| plotDiffHeatmap | Plot differential heatmap |
| plotDR | Plot reduced dimensions |
| plotEvents | Event plot |
| plotExprHeatmap | Plot expression heatmap |
| plotExprs | Expression densities |
| plotFreqHeatmap | Cluster frequency heatmap |
| plotMahal | Biaxial plot |
| plotMedExprs | Pseudobulk-level boxplot |
| plotMultiHeatmap | Multi-panel expression & frequency heatmaps |
| plotNRS | Plot non-redundancy scores |
| plotPbExprs | Pseudobulk-level boxplot |
| plotScatter | Scatter plot |
| plotSpillmat | Spillover matrix heatmap |
| plotYields | Yield plot |
| prepData | Data preparation |
| raw_data | Example data sets |
| runDR | Dimension reduction |
| sample_ff | Example data sets |
| sample_ids | 'SingleCellExperiment' accessors |
| sample_ids-method | 'SingleCellExperiment' accessors |
| sample_key | Example data sets |
| SCE-accessors | 'SingleCellExperiment' accessors |
| sce2fcs | SCE to 'flowFrame/Set' |
| ss_exp | Example data sets |
| state_markers | 'SingleCellExperiment' accessors |
| state_markers-method | 'SingleCellExperiment' accessors |
| type_markers | 'SingleCellExperiment' accessors |
| type_markers-method | 'SingleCellExperiment' accessors |