trajectory-based differential expression analysis for sequencing data

associationTest | Perform statistical test to check whether gene expression is... |

celltype | A vector defining cell types, used in the package vignette. |

clusterExpressionPatterns | Cluster gene expression patterns. |

conditionTest | Assess differential expression patterns between conditions... |

countMatrix | A count matrix, used in the package vignette. |

crv | A SlingshotDataset object, used in the package vignette. |

diffEndTest | Perform statistical test to check for DE between final stages... |

earlyDETest | Perform test of early differences between lineages |

evaluateK | Evaluate the optimal number of knots required for fitGAM. |

fitGAM | fitGAM |

gamList | A list of GAM models, used to demonstrate the various tests. |

getSmootherPvalues | Get smoother p-value as returned by 'mgcv'. |

getSmootherTestStats | Get smoother Chi-squared test statistics. |

nknots | knots |

patternTest | Assess differential expression pattern between lineages. |

plot_evalutateK_results | Evaluate an appropriate number of knots. |

plotGeneCount | Plot gene expression in reduced dimension. |

plotSmoothers | Plot the log-transformed counts and the fitted values for a... |

predictCells | predictCells |

predictSmooth | predictSmooth |

sds | A SlingshotDataset object, used in the package unit tests. |

startVsEndTest | Perform statistical test to check for DE between starting... |

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