SubpathwayLNCE: Identify Signal Subpathways Competitively Regulated by LncRNAs Based on ceRNA Theory

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Identify dysfunctional subpathways competitively regulated by lncRNAs through integrating lncRNA-mRNA expression profile and pathway topologies.

Author
Xinrui Shi, Chunquan Li and Xia Li
Date of publication
2016-01-19 08:17:59
Maintainer
Xinrui Shi <xinrui103@163.com>
License
GPL (>= 2)
Version
1.0

View on CRAN

Man pages

envData
The variables in the environment variable 'envData' of the...
getBackgroundLnc
Get the background of molecules
getExampleData
Get the environment data
getInteGraphList
Get the reconstructed signal pathway graphs
getInteUMGraph
Get the reconstructed condition-specific lncRNA-regulated...
getLncGenePairs
Get the co-express lncRNA-mRNA interactions
getLocSubGraphLnc
Get the located signal subpathways
identifyLncGraphW
Annotate and identify subpathways
plotAnnGraph
Visualize annotated pathway graphs
plotGraphL
Visualize a pathway graph
printGraphW
Print the results of graph annotation and identification
SubpathwayLNCE-internal
SubpathwayLNCE internal functions

Files in this package

SubpathwayLNCE
SubpathwayLNCE/inst
SubpathwayLNCE/inst/doc
SubpathwayLNCE/inst/doc/SubpathwayLNCE.Rnw
SubpathwayLNCE/inst/doc/SubpathwayLNCE.pdf
SubpathwayLNCE/inst/doc/SubpathwayLNCE.R
SubpathwayLNCE/NAMESPACE
SubpathwayLNCE/data
SubpathwayLNCE/data/envData.rda
SubpathwayLNCE/data/datalist
SubpathwayLNCE/R
SubpathwayLNCE/R/getLocSubGraphLnc.r
SubpathwayLNCE/R/getBackgroundLnc.r
SubpathwayLNCE/R/getEdgeLabel.r
SubpathwayLNCE/R/identifyLncGraphW.r
SubpathwayLNCE/R/getExampleData.r
SubpathwayLNCE/R/getKGeneFromGene.r
SubpathwayLNCE/R/getLncGenePairs.r
SubpathwayLNCE/R/getOneNodePath.r
SubpathwayLNCE/R/getEdgeLty.r
SubpathwayLNCE/R/plotAnnGraph.r
SubpathwayLNCE/R/getEnvironmentData.r
SubpathwayLNCE/R/printGraphW.r
SubpathwayLNCE/R/getNodeLabel.r
SubpathwayLNCE/R/getInteGraphList.r
SubpathwayLNCE/R/getInteUMGraph.r
SubpathwayLNCE/R/ExpProcess.r
SubpathwayLNCE/R/plotGraphL.r
SubpathwayLNCE/R/getLayout.r
SubpathwayLNCE/R/getSymbolFromGene.r
SubpathwayLNCE/vignettes
SubpathwayLNCE/vignettes/SubpathwayLNCE.Rnw
SubpathwayLNCE/MD5
SubpathwayLNCE/build
SubpathwayLNCE/build/vignette.rds
SubpathwayLNCE/DESCRIPTION
SubpathwayLNCE/man
SubpathwayLNCE/man/getExampleData.Rd
SubpathwayLNCE/man/getBackgroundLnc.Rd
SubpathwayLNCE/man/identifyLncGraphW.Rd
SubpathwayLNCE/man/plotGraphL.Rd
SubpathwayLNCE/man/envData.Rd
SubpathwayLNCE/man/SubpathwayLNCE-internal.Rd
SubpathwayLNCE/man/getLncGenePairs.Rd
SubpathwayLNCE/man/printGraphW.Rd
SubpathwayLNCE/man/getInteUMGraph.Rd
SubpathwayLNCE/man/getInteGraphList.Rd
SubpathwayLNCE/man/getLocSubGraphLnc.Rd
SubpathwayLNCE/man/plotAnnGraph.Rd