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 |