Cytometry dATa anALYSis Tools

adaptSpillmat | Adapt spillover matrix |

applyCutoffs | Single-cell debarcoding (2) |

assignPrelim | Single-cell debarcoding (1) |

cluster | FlowSOM clustering & ConsensusClusterPlus metaclustering |

compCytof | Compensate CyTOF data |

computeSpillmat | Compute spillover matrix |

concatFCS | FCS file Concatenation |

daFrame-class | Differential analysis frame class |

daFrame-methods | Extraction and replacement methods for objects of class... |

data | Example data sets |

dbFrame-class | Debarcoding frame class |

dbFrame-methods | Extraction and replacement methods for objects of class... |

estCutoffs | Estimation of distance separation cutoffs |

extractClusters | Extract clusters from a 'daFrame' |

filter | Filter daFrame |

guessPanel | Guess parameter panel |

launchGUI | Launch GUI |

mergeClusters | Manual cluster merging |

normCytof | Bead-based normalization |

outFCS | Write population-wise FCS files |

outFrames | Population-wise 'flowFrame's from a 'dbFrame' |

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 |

plotEvents | Event plot |

plotExprHeatmap | Plot expression heatmap |

plotExprs | Plot expressions |

plotMahal | Biaxial plot |

plotMDS | MDS plot |

plotMedExprs | Plot median expressions |

plotNRS | Plot non-redundancy scores |

plotSNE | plot t-SNE |

plotSpillmat | Spillover matrix heat map |

plotYields | Yield plot |

tSNE | Run t-SNE |

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