KSheu Library1

bed_to_granges | BED to GRanges |

calculate_signature_scores | calculate signature scores |

intersect_all | Intersects all lists |

intersect_doPCA_from_file_and_project_second_dataset | PCA from file and project second dataset |

intersect_log_doPCA_from_file_and_project_second_dataset | PCA from file and project second dataset after taking log of... |

log_PCA_from_file | PCA from file after taking log2 |

make_loadings_gctfile | Format PCA loadings for IGV |

make_rnk_file | Make .rnk file Input: txt file Output: writes out .rnk file |

make_scores_file | Makes scores file for IGV |

NNMF_from_file | Nonnegative matrix factorization |

PCA_from_file | PCA from file |

plot_pca | Plot PCA |

plot_pca_and_save | Plot PCA with save option |

plot_pca_projection | Plot PCA projection and data points from original PCA |

plot_pca_projection_all | Plot PCA projection and data points from original PCA with... |

plot_pca_projection_and_save | Plot PCA projection with save option |

plot_pca_projection_only | Plot PCA projection only |

plot_pls | Plot PLS |

PLSDA_from_file | Partial Least Squares from file |

PLSDA_from_file_and_predict_second_dataset | Partial Least Squares and predict second dataset |

PLSR_from_file | Partial Least Squares Regression from file Last mod: 6/17/18,... |

PLSR_from_file_and_predict_second_dataset | Partial Least Squares and predict second dataset |

varimax_from_file | Varimax rotation from file Last mod: 4/2018, ksheu |

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