Methods for Single-Cell RNA-Seq Data Analysis

buildSNNGraph | Build a SNN graph |

combineVar | Combine variance decompositions |

computeSpikeFactors | Normalization with spike-in counts |

computeSumFactors | Normalization by deconvolution |

convertTo | Convert to other classes |

correlatePairs | Test for significant correlations |

cyclone | Cell cycle phase classification |

decomposeVar | Decompose the gene-level variance |

denoisePCA | Denoise expression with PCA |

DM | Compute the distance-to-median statistic |

exploreData | Shiny app for explorative data analysis |

findMarkers | Find marker genes |

improvedCV2 | Stably model the technical coefficient of variation |

mnnCorrect | Mutual nearest neighbors correction |

overlapExprs | Overlap expression profiles |

quickCluster | Quick clustering of cells |

sandbag | Cell cycle phase training |

selectorPlot | Construct a selector plot via Shiny |

technicalCV2 | Model the technical coefficient of variation |

testVar | Test for significantly large variances |

trendVar | Fit a variance trend |

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