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

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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.

Author
Jing Yang, Hui Yu, Bao-Hong Liu, Zhongming Zhao, Lei Liu, Liang-Xiao Ma, Yi-Xue Li, Yuan-Yuan Li
Date of publication
2014-12-18 07:06:56
Maintainer
Bao-Hong Liu <bhliu@scbit.org>
License
GPL (> 2)
Version
2.1.2

View on CRAN

Man pages

ASC
Identify DCGs (Differential Coexpressed Genes) based on...
DCe
Identify DCGs (Differentially Coexpressed Genes) and DCLs...
DCGL-package
Differential Co-expression Analysis and Differential...
DCp
Identify DCGs (Differential Coexpressed Genes) based on the...
DCsum
Summarize DCGs and DCLs
DRplot
Visualization of DRLs
DRrank
Ranking Regulators by Target Enrichment Density (TED) and...
DRsort
Identify DRGs (Differential regulated Genes) and DRLs...
expressionBasedfilter
Filter genes according to expression level
exprs
Real dataset pulled down from GEO...
exprs_design
Experiment design of microarray matrix data
intgenelist
Interesting genes list
LFC
Select DCLs based on 'Limit Fold Change' model
LRC
Identify DCGs (Differential Coexpressed genes) based on 'Log...
percentLinkfilter
Filter gene coexpression links according to the top percent...
qLinkfilter
Filter gene coexpression links according to the q-values of...
RIF
Ranking Regulators by Regulator Impact Factor (RIF) Method
rLinkfilter
Filter gene coexpression links according to correlation...
tf2target
The dataset of human Transcription Factors regulate potential...
varianceBasedfilter
To filter genes according to expression variability
WGCNA
Identify DCGs (Differential Coexpressed Genes) based on the...

Files in this package

DCGL
DCGL/NAMESPACE
DCGL/data
DCGL/data/exprs_design.txt.gz
DCGL/data/intgenelist.RData
DCGL/data/tf2target.txt.gz
DCGL/data/tf2target.RData
DCGL/data/datalist
DCGL/data/exprs.RData
DCGL/data/exprs.txt.gz
DCGL/data/exprs_design.RData
DCGL/data/intgenelist.txt.gz
DCGL/R
DCGL/R/DCGL.r
DCGL/MD5
DCGL/DESCRIPTION
DCGL/man
DCGL/man/tf2target.Rd
DCGL/man/DCp.Rd
DCGL/man/ASC.Rd
DCGL/man/DRsort.Rd
DCGL/man/LFC.Rd
DCGL/man/qLinkfilter.Rd
DCGL/man/DRplot.Rd
DCGL/man/rLinkfilter.Rd
DCGL/man/expressionBasedfilter.Rd
DCGL/man/WGCNA.Rd
DCGL/man/intgenelist.Rd
DCGL/man/DRrank.Rd
DCGL/man/LRC.Rd
DCGL/man/exprs.Rd
DCGL/man/DCGL-package.Rd
DCGL/man/exprs_design.Rd
DCGL/man/DCe.Rd
DCGL/man/RIF.Rd
DCGL/man/DCsum.Rd
DCGL/man/percentLinkfilter.Rd
DCGL/man/varianceBasedfilter.Rd