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DCGL (version 1.0)

Differential Coexpression Analysis of Gene Expression Microarray Data

Description

Functions for basic differential coexpression analyses: gene filtering, link filtering, DCG (Differentially-Coexpressed Gene) identification and DCL (Differentially-Coexpressed Links) identification.Two algorithms,named DCP and DCe, are provided for DCG-identification or DCG and DCL-identification.

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Version

Install

install.packages('DCGL')

Monthly Downloads

59

Version

1.0

License

GPL (> 2)

Maintainer

BaoHong Liu

Last Published

August 19th, 2010

Functions in DCGL (1.0)

dataC

Simulated dataset based on deliberately-perturbed gene regulation networks (Yu, et al., 2010)
varianceBasedfilter

To filter genes according to expression variability
systematicLinkfilter

A systematic procedure for estimating a cutoff threshold of coexpression networks
dataA

Simulated dataset based on deliberately-perturbed gene regulation networks (Yu, et al., 2010)
LFC

Select DCLs based on 'Limit Fold Change' model
percentLinkfilter

To filter gene coexpression links according to the max expression correlation value
ASC

Identify DCGs (Differentially-Coexpressed genes) based on 'Average Specific Connection'
LRC

Identify DCGs (Differentially-Coexpressed genes) based on 'Log Ratio Connections'
dataB

Simulated dataset based on deliberately-perturbed gene regulation networks (Yu, et al., 2010)
qLinkfilter

To filter gene coexpression links according to the q-values of expression correlation values
DCGL-package

Differential Coexpression Analysis of Microarray Data
DCe

To identify DCGs (Differentially-Coexpressed Genes) and DCLs (Differentially-Coexpressed Links)
Simulated.ABC

Simulated datasets based on deliberately-perturbed gene regulation networks (Yu, et al., 2010)
expressionBasedfilter

To filter genes according to expression level
WGCNA

To identify DCGs (Differentially-Coexpressed genes) based on the 'Weighted Gene Coexpression Network Analysis'
DCp

To identify DCGs (Differentially-Coexpressed genes) based on the 'Differential Coexpression Profile'