Collection of Rudimentary Bioinformatics Tools


[Up] [Top]

Documentation for package ‘Corbi’ version 0.6-1

Help Pages

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