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
