Collection of Rudimentary Bioinformatics Tools

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Documentation for package ‘Corbi’ version 0.6-2

• 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