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A B C D E F G I L M N O P R S T Y
| adaptSpillmat | Adapt spillover matrix |
| adaptSpillmat-method | Adapt spillover matrix |
| applyCutoffs | Single-cell debarcoding (2) |
| applyCutoffs-method | Single-cell debarcoding (2) |
| assignPrelim | Single-cell debarcoding (1) |
| assignPrelim-method | Single-cell debarcoding (1) |
| bc_ids | Extraction and replacement methods for objects of class 'dbFrame' |
| bc_ids-method | Extraction and replacement methods for objects of class 'dbFrame' |
| bc_key | Extraction and replacement methods for objects of class 'dbFrame' |
| bc_key-method | Extraction and replacement methods for objects of class 'dbFrame' |
| cluster | 'FlowSOM' clustering & 'ConsensusClusterPlus' metaclustering |
| cluster_codes | 'SingleCellExperiment' convencience functions |
| cluster_codes-method | 'SingleCellExperiment' convencience functions |
| cluster_ids | 'SingleCellExperiment' convencience functions |
| cluster_ids-method | 'SingleCellExperiment' convencience functions |
| compCytof | Compensate CyTOF data |
| compCytof-method | Compensate CyTOF data |
| computeSpillmat | Compute spillover matrix |
| computeSpillmat-method | Compute spillover matrix |
| concatFCS | FCS file Concatenation |
| concatFCS-method | FCS file Concatenation |
| counts | Extraction and replacement methods for objects of class 'dbFrame' |
| counts-method | Extraction and replacement methods for objects of class 'dbFrame' |
| data | Example data sets |
| dbFrame | Debarcoding frame class |
| dbFrame-class | Debarcoding frame class |
| dbFrame-methods | Extraction and replacement methods for objects of class 'dbFrame' |
| deltas | Extraction and replacement methods for objects of class 'dbFrame' |
| deltas-method | Extraction and replacement methods for objects of class 'dbFrame' |
| ei | 'SingleCellExperiment' convencience functions |
| ei-method | 'SingleCellExperiment' convencience functions |
| estCutoffs | Estimation of distance separation cutoffs |
| estCutoffs-method | Estimation of distance separation cutoffs |
| exprs | 'SingleCellExperiment' convencience functions |
| exprs-method | Extraction and replacement methods for objects of class 'dbFrame' |
| extractClusters | Extract clusters from a 'SingleCellExperiment' |
| filterSCE | 'SingleCellExperiment' filtering |
| guessPanel | Guess parameter panel |
| guessPanel-method | Guess parameter panel |
| isotope_list | Example data sets |
| launchGUI | Launch GUI |
| marker_classes | 'SingleCellExperiment' convencience functions |
| marker_classes-method | 'SingleCellExperiment' convencience functions |
| mergeClusters | Manual cluster merging |
| merging_table | Example data sets |
| mhl_cutoff | Extraction and replacement methods for objects of class 'dbFrame' |
| mhl_cutoff-method | Extraction and replacement methods for objects of class 'dbFrame' |
| mhl_cutoff<- | Extraction and replacement methods for objects of class 'dbFrame' |
| mhl_cutoff<--method | Extraction and replacement methods for objects of class 'dbFrame' |
| mhl_dists | Extraction and replacement methods for objects of class 'dbFrame' |
| mhl_dists-method | Extraction and replacement methods for objects of class 'dbFrame' |
| mp_cells | Example data sets |
| normCytof | Bead-based normalization |
| normCytof-method | Bead-based normalization |
| normed_bcs | Extraction and replacement methods for objects of class 'dbFrame' |
| normed_bcs-method | Extraction and replacement methods for objects of class 'dbFrame' |
| n_cells | 'SingleCellExperiment' convencience functions |
| n_cells-method | 'SingleCellExperiment' convencience functions |
| outFCS | Write population-wise FCS files |
| outFCS-method | Write population-wise FCS files |
| outFrames | Population-wise 'flowFrame's from a 'dbFrame' |
| outFrames-method | Population-wise 'flowFrame's from a 'dbFrame' |
| PBMC_fs | Example data sets |
| PBMC_md | Example data sets |
| PBMC_panel | Example data sets |
| 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 |
| plotEvents-method | Event plot |
| plotExprHeatmap | Plot expression heatmap |
| plotExprs | Plot expressions |
| plotMahal | Biaxial plot |
| plotMahal-method | Biaxial plot |
| plotMDS | MDS plot |
| plotMedExprs | Plot median expressions |
| plotNRS | Plot non-redundancy scores |
| plotSpillmat | Spillover matrix heat map |
| plotSpillmat-method | Spillover matrix heat map |
| plotYields | Yield plot |
| plotYields-method | Yield plot |
| prepData | Data preparation |
| raw_data | Example data sets |
| runDR | Dimension reduction |
| sample_ff | Example data sets |
| sample_ids | 'SingleCellExperiment' convencience functions |
| sample_ids-method | 'SingleCellExperiment' convencience functions |
| sample_key | Example data sets |
| sep_cutoffs | Extraction and replacement methods for objects of class 'dbFrame' |
| sep_cutoffs-method | Extraction and replacement methods for objects of class 'dbFrame' |
| sep_cutoffs<- | Extraction and replacement methods for objects of class 'dbFrame' |
| sep_cutoffs<--method | Extraction and replacement methods for objects of class 'dbFrame' |
| ss_exp | Example data sets |
| state_markers | 'SingleCellExperiment' convencience functions |
| state_markers-method | 'SingleCellExperiment' convencience functions |
| type_markers | 'SingleCellExperiment' convencience functions |
| type_markers-method | 'SingleCellExperiment' convencience functions |
| yields | Extraction and replacement methods for objects of class 'dbFrame' |
| yields-method | Extraction and replacement methods for objects of class 'dbFrame' |