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DCGL (version 2.1.2)

Differential Co-expression Analysis and Differential Regulation Analysis of Gene Expression Microarray Data

Description

Functions for 1) gene filtration; 2) link filtration; 3) differential co-expression analysis: DCG (Differential Coexpressed Gene) identification and DCL (Differentially Coexpressed Link) identification; and 4) differential regulation analysis: DRG (Differential Regulated Gene) identification, DRL (Differential Regulated Link) identification, DRL visualization and regulator ranking.

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Version

Install

install.packages('DCGL')

Monthly Downloads

110

Version

2.1.2

License

GPL (> 2)

Maintainer

BaoHong Liu

Last Published

December 18th, 2014

Functions in DCGL (2.1.2)

ASC

Identify DCGs (Differential Coexpressed Genes) based on 'Average Specific Connection'
DRplot

Visualization of DRLs
DCe

Identify DCGs (Differentially Coexpressed Genes) and DCLs (Differentially Coexpressed Links)
LRC

Identify DCGs (Differential Coexpressed genes) based on 'Log Ratio Connections'
RIF

Ranking Regulators by Regulator Impact Factor (RIF) Method
qLinkfilter

Filter gene coexpression links according to the q-values of expression correlation values
exprs

Real dataset pulled down from GEO (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE17967)
expressionBasedfilter

Filter genes according to expression level
DCsum

Summarize DCGs and DCLs
varianceBasedfilter

To filter genes according to expression variability
tf2target

The dataset of human Transcription Factors regulate potential target genes
LFC

Select DCLs based on 'Limit Fold Change' model
DCp

Identify DCGs (Differential Coexpressed Genes) based on the 'Differential Coexpression Profile'
WGCNA

Identify DCGs (Differential Coexpressed Genes) based on the 'Weighted Gene Coexpression Network Analysis'
DRsort

Identify DRGs (Differential regulated Genes) and DRLs (Differential regulated Links)
DCGL-package

Differential Co-expression Analysis and Differential Regulation Analysis of Gene Expression Microarray Data
exprs_design

Experiment design of microarray matrix data
rLinkfilter

Filter gene coexpression links according to correlation coefficient value
percentLinkfilter

Filter gene coexpression links according to the top percent of expression correlation coefficient value
DRrank

Ranking Regulators by Target Enrichment Density (TED) and Targets' DCL Density (TDD)
intgenelist

Interesting genes list