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README

Corbi is an R package provided a bundle of basic and fundamental bioinformatics tools, such as differential expression analysis, biomarker identification, network querying and alignment, subnetwork extraction and search.

How to install?

How to use?

There are documentation available within package. To read the documents in the R terminal using the command ?Corbi

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Install

install.packages('Corbi')

Monthly Downloads

65

Version

0.6-0

License

GPL (>= 2)

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Maintainer

LingYun Wu

Last Published

June 13th, 2020

Functions in Corbi (0.6-0)

get_ratio_distribution2

Calculate expression ratio distribution
make_DEG_pattern

Simulate differentially expressed gene pattern
extend_subnets

Extend subnetworks from smaller subnetworks
markrank

MarkRank
get_shortest_distances

Calculate shortest distances of unweighted network
simulate_dropout

Simulate dropout expression data
simulate_dropout2

Simulate dropout expression data
get_ratio_variance

Calculate expression ratio variances
pmultihyper

The Multivariate Hypergeometric Distribution
pmultinom

The Multinomial Distribution
simulate_sample_groups

Simulate sample groups from given samples with labels
get_subnets

All subnetworks of limited size
kappa_score

Cohen's kappa score
make_DEG_data

Simulate differentially expressed gene data (Gaussian)
netDEG

netDEG: Differentially expressed gene identification method
net_align

Network alignment method based on conditional random fields
net_query

Network querying method based on conditional random fields
make_DEG_data2

Simulate differentially expressed gene data (Negative binomial)
nnzero

The number of non-zero values of a submatrix
write_net

Write network information to text file
read_net

Read network information from text file
netDEG_pvalue

Calculate netDEG p-values
rmultihyper

The Multivariate Hypergeometric Distribution
submatrix

Extract a submatrix from a matrix
p_combine

Calculate combined p-value
best_subnets

The best subnetworks
column

Extract a column from a matrix
get_ratio_distribution

Calculate expression ratio distribution
URG_normalize

Normalize using given factors
URG_getFactor

Calculate normalization factors for URG method
Corbi-package

Corbi - Collection of Rudimentary Bioinformatics Tools
get_adjusted_deg_diff

Calculate adjusted degree differences for given network
get_diff_ratio_net

Construct differential expression ratio network