| Function | Description |
| ABPkgBuilder | Functions that support a single API for building data packages |
| addNamespace | Functions to add namespaces for data files or seal the environment objects in the data subdirectory |
| athPkgBuilder | Functions that build annotation packages for Arbidopsis |
| chrLocPkgBuilder | A function to build a data package containing mappings between LocusLink ids and the chromosomal locations of genes represented by the LocusLink ids |
| cleanSrcObjs | Supporting function that may no of any other usese |
| cMapPathBuilder | Functions that build a data pacakge using data provided by cMAP |
| cols2Env | Creates a environment object using data from two columns of a matrix |
| descriptionInfo | Detailed DESCRIPTION Information |
| downloadSourceData | Create a local mirror of annotation data sources |
| EG-class | Class "EG" handles data provided by Entrez Gene |
| 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. |
| GEO-class | Class "GEO" represents a GEO object that reads/downloads data from the GEO web site |
| getChroLocation | Functions to extract data from Golden Path |
| getDPStats | Functions to read in the statistics about a data package |
| getKEGGIDNName | Functions to get/process pathway and enzyme data from KEGG |
| getPubDataGo | Functions to download public domain annotation data sources |
| 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 |
| getUGShortName | Functions that produce short versions of organism names used by UniGene or for other purposes |
| getYeastData | Functions to get/process yeast genome data |
| GO-class | Class "GO" a class to handle data from Gene Ontology |
| GOPkgBuilder | Functions to build a data package using GO data |
| GOXMLParser | Parse the Gene Ontology OBO XML data file |
| GP-class | Class "GP" a sub-class of pubRepo to get/process data from GoldenPath |
| HG-class | Class "HG" a class to represent HomoloGene data source |
| homoPkgBuilder | Functions to build a homology data package using data from NCBI |
| IPI-class | Class "IPI" a sub-class of pubRepo to handle data from International Protein Index (IPI) |
| 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 |
| loadFromUrl | Functions to load files from a web site |
| makeLLDB | Create a lazy loading database for package data files |
| 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 |
| MeSHParser | Function to parse the XML data file form MeSH |
| print.ABQCList | Prints the quality control results for a given data package in a nice format |
| pubDataURLs | Public Domain Data Source URLs |
| 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 |
| readSourceUrlConfig | Read a data source URL config file |
| resolveMaps | Functions to obtain unified mappings for a given set of ids using various sources |
| sourceURLs | A data file contains urls for data available from various public repositories |
| 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 |
| unifyMappings | A function to unify mapping result from different sources |
| wget | Wrapper for system wget |
| writeChrLength | Functions that creates binary files for chromosome length and organism |
| writeHomoXMLData | Functions to parse HomoloGene XML data file and build the homology annotation data package |
| writeManPage | Functions that write supporting files needed by a data package |
| writeSourceUrlConfig | Create a source URL config file |
| 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 |
| YG-class | Class "YG" a sub-class of pubRepo that reads/downloads data from yeast genomic |