Identify Signal Subpathways Competitively Regulated by LncRNAs
Based on ceRNA Theory
Identify dysfunctional subpathways competitively regulated by lncRNAs through integrating lncRNA-mRNA expression profile and pathway topologies.
R (>= 2.10), igraph, RBGL, utils, BiasedUrn, graph, graphics,
stats
ExpProcess.r getBackgroundLnc.r getEdgeLabel.r getEdgeLty.r
getEnvironmentData.r getInteGraphList.r getInteUMGraph.r
getKGeneFromGene.r getLayout.r getLncGenePairs.r
getExampleData.r getLocSubGraphLnc.r getNodeLabel.r
getOneNodePath.r getSymbolFromGene.r identifyLncGraphW.r
plotAnnGraph.r plotGraphL.r printGraphW.r
Statistics, SuPathways, LncRNAs, enrichment analysis,ceRNA

Annotation and Identification of the KEGG pathway.
SubpathwayMiner facilitates sub-pathway annotation and identification of metabolic pathways. It also provides annotation and identification of entire pathways.
ann.R initialize.R subGraph.R id.R graph.R go2go.R visualize.R

Annotation and identification of the KEGG pathways.

SubpathwayMiner is an R-based software for flexible
pathway identification. (1) SubpathwayMiner can provide users
with sub-pathway annotation and identification of metabolic
pathways based on enzyme commission (EC) numbers. (2)
SubpathwayMiner can provide users with sub-pathway annotation
and identification based on KEGG Orthology (KO) identifiers.
(new!) (3) SubpathwayMiner can provide annotation and
identification of entire pathways. (4) SubpathwayMiner can
support most of organisms in the KEGG GENE database. (5) Data
can be automatically updated on demand by the user.
ann.R initialize.R subGraph.R id.R graph.R go2go.R visualize.R
ko.R

Identification of Disease related sub-pathways from the KEGG
pathways.
SubpathwayMiner is an R-based software for flexible
pathway identification. (1) SubpathwayMiner can provide users
with sub-pathway annotation and identification of metabolic
pathways based on enzyme commission (EC) numbers. (2)
SubpathwayMiner can provide users with sub-pathway annotation
and identification based on KEGG Orthology (KO) identifiers.
(3) SubpathwayMiner can provide annotation and identification
of entire pathways. (4) SubpathwayMiner can support most of
organisms in the KEGG GENE database. (5) Data can be
automatically updated on demand by the user. (6)
SubpathwayMiner can provide identification of disease related
sub-pathways.
D2P.R ann.R initialize.R subGraph.R id.R graph.R go2go.R
visualize.R ko.R