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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
2.1.2
2.1.1
2.1.0
2.0.2
2.0.1
1.02
1.01
1.0
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Install
install.packages('DCGL')
Monthly Downloads
83
Version
2.1.2
License
GPL (> 2)
Maintainer
BaoHong Liu
Last Published
December 18th, 2014
Functions in DCGL (2.1.2)
Search functions
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