ABPkgBuilder            Functions that support a single API for
                        building data packages
GEO-class               Class "GEO" represents a GEO object that
                        reads/downloads data from the GEO web site
GO-class                Class "GO" a class to handle data from Gene
                        Ontology
GOPkgBuilder            A functions to builder a data package using GO
                        data
GOXMLParser             Functions to read/parse the XML document of
                        Gene Ontology data
GP-class                Class "GP" a sub-class of pubRepo to
                        get/process data from GoldenPath
KEGG-class              Class "KEGG" a sub-class of pubRepo to
                        get/process pathway and enzyme information
KEGGPkgbuilder          A function to make the data package for KEGG
LL-class                Class "LL" a sub-class of pubRepo to handle
                        data from LocusLink
SPPkgBuilder            A function to build a data pckage using
                        Swiss-Prot protein data
UG-class                Class "UG" a sub-class of pubRepo to handle
                        data from UniGene
YG-class                Class "YG" a sub-class of pubRepo that
                        reads/downloads data from yeast genomic
chrLocPkgBuilder        A function to build a data package containing
                        mappings between LocusLink ids and the
                        chromosomal locations of genes represented by
                        the LocusLink ids
cols2Env                Creates a environment object using data from
                        two columns of a matrix
fileMuncher             Dynamically create a Perl script to parse a
                        source file base on user specifications
fileToXML               A function to convert a text file to XML.
getChroLocation         Functions to extract data from golden path
getDPStats              A function to read in the statistics about a
                        data package
getKEGGIDNName          Functions to get/process pathway and enzyme
                        data from KEGG
getSrcBuilt             Functions that get the built date or number of
                        the source data used for annotation
getSrcUrl               Functions that find the correct url for
                        downloading annotation data
getYeastData            Functions to get/process yeast genome data
homoPS-class            Class "homoPS"
homoPkgBuilder          Functions to build a homology data package
                        using data from NCBI
loadFromUrl             Functions to load files from a web site
makeSrcInfo             Functions to make source information available
                        for later use
map2LL                  A function that maps LocusLink ids to other
                        public repository ids and vice versa
print.ABQCList          Prints the quality control results for a given
                        data package in a nice format
pubRepo-class           Class "pubRepo" a generic class for
                        downloading/parsing data provided by various
                        public data repositories
queryGEO                Function to extract a data file from the GEO
                        web site
resolveMaps             Functions to obtain unified mappings between
                        ids
sourceURLs              A data file contains urls for data available
                        from various public repositories
unifyMappings           A function to unify mapping result from
                        different sources
writeChrLength          Functions that creates binary files for
                        chromosome length and organism
writeManPage            Functions that write supporting files needed
                        by a data package
writeXMLHeader          A function to write header information to an
                        XML file.
yeastAnn                Functions to annotate yeast genom data
yeastPkgBuilder         Functions to do a data package for yeast
                        genome
