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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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Version

Install

install.packages('Corbi')

Monthly Downloads

65

Version

0.6-2

License

GPL (>= 2)

Issues

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Maintainer

LingYun Wu

Last Published

May 30th, 2022

Functions in Corbi (0.6-2)

column

Extract a column from a matrix
get_diff_ratio_net

Construct differential expression ratio network
netDEG

netDEG: Differentially expressed gene identification method
best_subnets

The best subnetworks
kappa_score

Cohen's kappa score
net_query

Network querying method based on conditional random fields
net_align

Network alignment method based on conditional random fields
get_subnets

All subnetworks of limited size
make_DEG_data

Simulate differentially expressed gene data (Gaussian)
nnzero

The number of non-zero values of a submatrix
make_DEG_data2

Simulate differentially expressed gene data (Negative binomial)
write_net

Write network information to text file
p_combine

Calculate combined p-value
get_ratio_variance

Calculate expression ratio variances
simulate_dropout

Simulate dropout expression data
simulate_dropout2

Simulate dropout expression data
netDEG_pvalue

Calculate netDEG p-values
get_shortest_distances

Calculate shortest distances of unweighted network
markrank

MarkRank
read_net

Read network information from text file
simulate_sample_groups

Simulate sample groups from given samples with labels
make_DEG_pattern

Simulate differentially expressed gene pattern
rmultihyper

The Multivariate Hypergeometric Distribution
pmultihyper

The Multivariate Hypergeometric Distribution
pmultinom

The Multinomial Distribution
submatrix

Extract a submatrix from a matrix
URG_normalize

Normalize using given factors
get_adjusted_deg_diff

Calculate adjusted degree differences for given network
get_ratio_distribution

Calculate expression ratio distribution
get_ratio_distribution2

Calculate expression ratio distribution
Corbi-package

Corbi - Collection of Rudimentary Bioinformatics Tools
extend_subnets

Extend subnetworks from smaller subnetworks
URG_getFactor

Calculate normalization factors for URG method