Corbi-package |
Corbi - Collection of Rudimentary Bioinformatics Tools |

best_subnets |
The best subnetworks |

column |
Extract a column from a matrix |

Corbi |
Corbi - Collection of Rudimentary Bioinformatics Tools |

extend_subnets |
Extend subnetworks from smaller subnetworks |

get_adjusted_deg_diff |
Calculate adjusted degree differences for given network |

get_diff_ratio_net |
Construct differential expression ratio network |

get_ratio_distribution |
Calculate expression ratio distribution |

get_ratio_distribution2 |
Calculate expression ratio distribution |

get_ratio_variance |
Calculate expression ratio variances |

get_shortest_distances |
Calculate shortest distances of unweighted network |

get_subnets |
All subnetworks of limited size |

kappa_score |
Cohen's kappa score |

make_DEG_data |
Simulate differentially expressed gene data (Gaussian) |

make_DEG_data2 |
Simulate differentially expressed gene data (Negative binomial) |

make_DEG_pattern |
Simulate differentially expressed gene pattern |

markrank |
MarkRank |

netDEG |
netDEG: Differentially expressed gene identification method |

netDEG_pvalue |
Calculate netDEG p-values |

net_align |
Network alignment method based on conditional random fields |

net_query |
Network querying method based on conditional random fields |

net_query_batch |
Network querying method based on conditional random fields |

nnzero |
The number of non-zero values of a submatrix |

pmultihyper |
The Multivariate Hypergeometric Distribution |

pmultinom |
The Multinomial Distribution |

p_combine |
Calculate combined p-value |

read_net |
Read network information from text file |

rmultihyper |
The Multivariate Hypergeometric Distribution |

simulate_dropout |
Simulate dropout expression data |

simulate_dropout2 |
Simulate dropout expression data |

simulate_sample_groups |
Simulate sample groups from given samples with labels |

submatrix |
Extract a submatrix from a matrix |

URG_getFactor |
Calculate normalization factors for URG method |

URG_normalize |
Normalize using given factors |

write_net |
Write network information to text file |