Title: Identify Signal Subpathways Competitively Regulated by LncRNAs
Author: Xinrui Shi, Chunquan Li and Xia Li
Description: Identify dysfunctional subpathways competitively regulated by lncRNAs through integrating lncRNA-mRNA expression profile and pathway topologies.
Depends: R (>= 2.10), igraph, RBGL, utils, BiasedUrn, graph, graphics,
Collate: ExpProcess.r getBackgroundLnc.r getEdgeLabel.r getEdgeLty.r
biocViews: Statistics, SuPathways, LncRNAs, enrichment analysis,ceRNA
Packaged: 2016-01-19 01:50:31 UTC; Administrator

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

Title: Annotation and identification of the KEGG pathways.

Description: 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.

Title: Identification of Disease related sub-pathways from the KEGG
(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
Collate: D2P.R ann.R initialize.R subGraph.R id.R graph.R go2go.R

Package: SubpathwayMiner
Version: 3.1
Title: A software package for annotation and identification of the KEGG
pathways.
Author: Chunquan Li
Maintainer: Chunquan Li <lcqbio@yahoo.com.cn>
Description: 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.(new!) The version 3.1 use a new approach to store
organism-related data (e.g., gene-enzyme relation data), which
make the running time of the function updateOrgAndIdType reduce
significantly compared with the old version. Therefore, the
environment variables of organisms will be provided no longer
for reducing size of the software package. When using this
tool, please cite: Li, C., Li, X., Miao, Y., Wang, Q., Jiang,
W., Xu, C., Li, J., Han, J., Zhang, F., Gong, B. et al. (2009)
SubpathwayMiner: a software package for flexible identification
of pathways. Nucleic Acids Res, 37, e131. Full text:
http://nar.oxfordjournals.org/cgi/content/full/37/19/e131
Depends: R(>= 2.8.0),RBGL(>= 1.18.0),fdrtool(>= 1.2.4),utils
Suggests: Rgraphviz(>= 1.20.3),XML(>= 1.94)
Collate: D2P.R ann.R initialize.R subGraph.R graph.R go2go.R
visualize.R ko.R
License: GPL (>= 2)
biocViews: Statistics, Annotation
Packaged: 2010-08-31 10:24:37 UTC; jrc
Repository: CRAN
Date/Publication: 2010-09-01 06:44:31