R: Collection of Rudimentary Bioinformatics Tools

# Collection of Rudimentary Bioinformatics Tools

## Documentation for package ‘Corbi’ version 0.6-1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## 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