Utility Functions for RNASeq Data Analysis

create_mst_igraphs_for_samples | Generate Minimum spanning trees from expression matrices |

examine_dataset | Generate several plots and objects for dataset exploration |

explore_expression | View expression of genes on 2D plots. |

get_cellranger_matrices | Loads the matrix files from a 10X run |

get_cidr_distance_matrix_from_raw_counts | Compute distance between samples |

get_cluster_by_ensembl_mat_of_expr_summaries | calculate cluster summaries |

get_df_of_cluster_enrichments_for_each_gene | Determine genes enriched in regions of a minimum spanning... |

get_mean_dist_from_matrix | The function calculates and returns the mean of the... |

get_normalized_expression_matrix | Process cellranger output |

get_random_genes_from_matrix | Filter random genes from matrix |

read_merge_and_return_sample_matrices | Loads and merges the matrix files from a 10X run |

remove_ribosomal_proteins_and_mitochondrial_genes_from_matrix | Filter MT and Ribsomal protein genes |

run_interactive_monocle_gadget | Explore a dataset with monocle |

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