The usually used code for data analysis in my pipeline.

gene_filter | Gene Filter |

mad_filter | MAD Filter |

normalPCA | Principal Component Analysis |

onestepPCA | Principal Component Analysis |

outlier_connectivity | Sample filter based on connectivity z-socres |

outlier_hcluster | Sample filter based on hierarchical clustering |

outlier_PCA | Sample filter based on PCA |

pvca | Principal Variance Component Analysis |

pvca2 | Principal Variance Component Analysis 2 |

QC_boxplot | Box plot and bar plot |

QC_density | Density plot |

shinyDensity | Shiny density plot |

shinyHcluster | Shiny hierarchical clustering |

shinyHcluster2 | Shiny hierarchical clustering 2 |

shinyPCA | Shiny PCA |

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