Package: iSubpathwayMiner
Version: 2.0
Title: The package can implement the graph-based reconstruction,
analyses, and visualization of the KEGG pathways.
Author: Chunquan Li
Maintainer: Chunquan Li <lcqbio@yahoo.com.cn>
Description: The package can implement the graph-based reconstruction,
analyses, and visualization of the KEGG pathways. (1) Our
system provides many strategies of converting pathways to graph
models. Ten functions related to conversion from pathways to
graphs are developed. Furthermore, the combinations of these
functions can get many combined conversion strategies of
pathway graphs (> 20). (2) The iSubpathwayMiner can support the
annotation and identification of pathways based on gene sets,
compound sets, and even the combined sets of genes and
compounds. The entire pathway and subpathway identification
methods are available for these sets. (3) The system can also
support topology-based pathway analysis of these sets. (4) We
develop KEGG layout style of pathway graphs in R to simulate
the layout of the pathway picture in KEGG website. In addition,
our system has also provided many types of automatic layout
styles. Pathway graphs can also be exported to the GML format
supported by Cytoscape. (5) The iSubpathwayMiner can provide
the most up-to-date pathway analysis results for users.
Multiple species (about 139 Eukaryotes, 1141 Bacteria and 93
Archaea) and different gene identifiers (KEGG compound, Entrez
Gene IDs, gene official symbol, NCBI-gi IDs, UniProt IDs, PDB
IDs, etc.) can also be supported by the system.
Depends: R (>= 2.10.0),graph,RBGL,igraph,XML,utils
Collate: initialize.R visualize.R go2go.R pathway.R metabolic.R
non-metabolic.R metabolic_non-metabolic.R annotation.R
subpathway-method.R topologicalanalysis.R combindedNetwork.R
sample.R
LazyData: Yes
License: GPL (>= 2)
biocViews: Statistics, Annotation, Pathways, Graphs, Networks
Packaged: 2012-02-20 16:18:22 UTC; Administrator
Repository: CRAN
Date/Publication: 2012-02-20 20:06:23

Package: iSubpathwayMiner
Version: 3.0
Title: The package can implement the graph-based reconstruction and
analyses of the KEGG pathways.
Author: Chunquan Li
Maintainer: Chunquan Li <lcqbio@yahoo.com.cn>
Description: The package can implement the graph-based reconstruction
and analysis of the KEGG pathways. (1) Our system provides many
strategies of converting pathways to graph models. Ten
functions related to conversion from pathways to graphs are
developed. Furthermore, the combinations of these functions can
get many combined conversion strategies of pathway graphs (>
20). The system can also support topology-based pathway
analysis of molecule sets. (2) The iSubpathwayMiner can support
the annotation and identification of entire pathways based on
molecule (gene and/or metabolite) sets. (3) The
iSubpathwayMiner provides the k-clique method for
identification of metabolic subpathways based on gene sets. (4)
The iSubpathwayMiner provides the Subpathway-GM method for
identification of metabolic subpathways based on gene and
metabolite sets (new!).
Depends: R (>= 2.15.1),graph,RBGL,igraph,XML,utils
Collate: initialize.R visualize.R go2go.R pathway.R metabolic.R
non-metabolic.R metabolic_non-metabolic.R annotation.R
topologicalanalysis.R combindedNetwork.R sample.R k-clique.R
SubpathwayGM.R
LazyData: Yes
License: GPL (>= 2)
biocViews: Statistics, Annotation, Pathways, Graphs, Networks
Packaged: 2012-07-08 02:47:08 UTC; Administrator
Repository: CRAN
Date/Publication: 2012-07-08 06:21:22