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 |