Network smoothing for scRNAseq

calc2DEntropy | Calculate entropy in 2D data |

clusterExperimentWorkflow | Performs clustering workflow using 'clusterExperiment'... |

clusterOne | Run one clustering using kmeans o PAM |

dimReduce | Get lower dimension embedding |

human.ppi | Human Protein-Protein interaction graph |

l1NormalizeColumns | Column-normalize a sparse, symmetric matrix (using the l1... |

l1NormalizeRows | Row-normalize a sparse, symmetric matrix (using the l1 norm)... |

mouse.ppi | Mouse Protein-Protein interaction graph |

netSmooth | Perform network smoothing of gene expression or other omics... |

pickDimReduction | Pick the dimensionality reduction method for a dataset that... |

projectFromNetworkRecombine | Combine gene expression from smoothed space (that of the... |

projectOnNetwork | Project the gene expression matrix onto a lower space of the... |

randomWalkByIterations | Smooth data on graph by computing iterations |

randomWalkByMatrixInv | Smooth data on graph by computing the closed-form steady... |

randomWalkBySolve-matrix-method | Smooth data on graph by solving the linear equation (I -... |

robustClusters | Perform robust clustering on dataset, and calculate the... |

scoreSmoothing | Calculate a score for a smoothing result, for picking the... |

smallPPI | A small human Protein-Protein interaction graph for use in... |

smallscRNAseq | A small single cell RNA-seq dataset for use in examples. |

smoothAndRecombine | Perform network smoothing on network when the network genes... |

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