Package: iSubpathwayMiner
Version: 1.0
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(>= 1.24.0),RBGL(>= 1.24.0),igraph(>=
        0.5.2),XML(>= 3.1-0),fdrtool(>= 1.2.4),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
License: GPL (>= 2)
biocViews: Statistics, Annotation, Pathways, Graphs, Networks
Packaged: 2012-01-06 12:28:28 UTC; ripley
Repository: CRAN
Date/Publication: 2012-01-06 12:29:46
