A B C D E F G H I K L M N O P Q R S T U V W Y
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 |
baseFile | Class "pubRepo" a generic class for downloading/parsing data provided by various public data repositories |
baseFile,pubRepo-method | Class "pubRepo" a generic class for downloading/parsing data provided by various public data repositories |
baseFile<-,pubRepo-method | Class "pubRepo" a generic class for downloading/parsing data provided by various public data repositories |
builtInfo | Class "pubRepo" a generic class for downloading/parsing data provided by various public data repositories |
builtInfo,pubRepo-method | Class "pubRepo" a generic class for downloading/parsing data provided by various public data repositories |
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 |
cMAPParser | Functions that build a data pacakge using data provided by cMAP |
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 |
copyTemplates | Functions to build a data package using GO data |
countMapping | Functions to read in the statistics about a data package |
createEmptyDPkg | Functions that support a single API for building data packages |
descriptionInfo | Detailed DESCRIPTION Information |
downloadData | Class "pubRepo" a generic class for downloading/parsing data provided by various public data repositories |
downloadData,pubRepo-method | Class "pubRepo" a generic class for downloading/parsing data provided by various public data repositories |
downloadSourceData | Create a local mirror of annotation data sources |
EG | Class "EG" handles data provided by Entrez Gene |
EG-class | Class "EG" handles data provided by Entrez Gene |
escapeLatexChr | Functions that write supporting files needed by a data package |
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. |
findChrLength | Functions that creates binary files for chromosome length and organism |
findIDNPath | Class "KEGG" a sub-class of pubRepo to get/process pathway and enzyme information |
findIDNPath,KEGG-method | Class "KEGG" a sub-class of pubRepo to get/process pathway and enzyme information |
findNumCol | Functions to get/process yeast genome data |
findYGChrLength | Functions to do a data package for yeast genome |
formatABQCList | Functions to read in the statistics about a data package |
formatChrLoc | Functions to annotate yeast genom data |
formatGO | Functions to annotate yeast genom data |
formatName | Functions that write supporting files needed by a data package |
fromWeb | Class "pubRepo" a generic class for downloading/parsing data provided by various public data repositories |
fromWeb,pubRepo-method | Class "pubRepo" a generic class for downloading/parsing data provided by various public data repositories |
fromWeb<-,pubRepo-method | Class "pubRepo" a generic class for downloading/parsing data provided by various public data repositories |
GEO | Class "GEO" represents a GEO object that reads/downloads data from the GEO web site |
GEO-class | Class "GEO" represents a GEO object that reads/downloads data from the GEO web site |
getAllRdaName | Functions that write supporting files needed by a data package |
getAllSrc | Functions to make source information available for later use |
getAllUrl | Functions that find the correct url for downloading annotation data |
getAnnData | Supporting function that may no of any other usese |
getBaseFile | Supporting function that may no of any other usese |
getBaseParsers | Functions that support a single API for building data packages |
getBuild4Yeast | Functions that write supporting files needed by a data package |
getChrLenghts | Functions that support a single API for building data packages |
getChrLengths | Functions that support a single API for building data packages |
getChrNum | A function to build a data package containing mappings between LocusLink ids and the chromosomal locations of genes represented by the LocusLink ids |
getChroLocation | Functions to extract data from Golden Path |
getChroms4Org | A function to build a data package containing mappings between LocusLink ids and the chromosomal locations of genes represented by the LocusLink ids |
getCytoList | Functions to extract data from Golden Path |
getCytoLoc | Functions to extract data from Golden Path |
getDate | Functions to read in the statistics about a data package |
getDetailV | A function to build a data pckage using Swiss-Prot protein data |
getDirContent | Functions that support a single API for building data packages |
getDPStats | Functions to read in the statistics about a data package |
getDSrc | Functions that write supporting files needed by a data package |
getDsrc | Functions that write supporting files needed by a data package |
getEGAccName | Functions that support a single API for building data packages |
getEGBuilt | Functions that get the built date or number of the source data used for annotation |
getEGUrl | Functions that find the correct url for downloading annotation data |
getEIdNName | A function to make the data package for KEGG |
getEnvNames | A function to build a data pckage using Swiss-Prot protein data |
getExample | Functions that write supporting files needed by a data package |
getExten | A function that maps LocusLink ids to other public repository ids and vice versa |
getGEOUrl | Functions that find the correct url for downloading annotation data |
getGEOYeast | Functions to annotate yeast genom data |
getGOBuilt | Functions that get the built date or number of the source data used for annotation |
getGOUrl | Functions that find the correct url for downloading annotation data |
getGPData | Functions to extract data from Golden Path |
getHGBuilt | Functions that get the built date or number of the source data used for annotation |
getHGUrl | Functions that find the correct url for downloading annotation data |
getHomoData | Functions to build a homology data package using data from NCBI |
getHomoDList | Functions to build a homology data package using data from NCBI |
getHomoPS | Functions to build a homology data package using data from NCBI |
getHumanChrLengths | Functions that support a single API for building data packages |
getIntIDMapping | Functions to build a homology data package using data from NCBI |
getItem | Functions that write supporting files needed by a data package |
getKEGGBuilt | Functions that get the built date or number of the source data used for annotation |
getKEGGFile | A function to make the data package for KEGG |
getKEGGGeneMap | A function to make the data package for KEGG |
getKEGGIDNName | Functions to get/process pathway and enzyme data from KEGG |
getKEGGOrgName | Functions to get/process pathway and enzyme data from KEGG |
getKEGGUrl | Functions that find the correct url for downloading annotation data |
getList4GO | Functions that support a single API for building data packages |
getLL2ACC | A function that maps LocusLink ids to other public repository ids and vice versa |
getLL2IntID | Functions to build a homology data package using data from NCBI |
getLLBuilt | Functions that get the built date or number of the source data used for annotation |
getLLNGBMap | Supporting function that may no of any other usese |
getLLPathMap | Functions to get/process pathway and enzyme data from KEGG |
getLLUrl | Functions that find the correct url for downloading annotation data |
getMouseChrLengths | Functions that support a single API for building data packages |
getMultiColNames | Functions that support a single API for building data packages |
getNoDup | Functions to obtain unified mappings for a given set of ids using various sources |
getOneMap | Functions that build annotation packages for Arbidopsis |
getOrgName | A function that maps LocusLink ids to other public repository ids and vice versa |
getOrgNameNCode | Functions to build a homology data package using data from NCBI |
getPBased | Functions to read in the statistics about a data package |
getProbe2SGD | Functions to annotate yeast genom data |
getProbeNum | Functions to read in the statistics about a data package |
getPubDataEntrezGene | Functions to download public domain annotation data sources |
getPubDataGo | Functions to download public domain annotation data sources |
getPubDataGoldenPath | Functions to download public domain annotation data sources |
getPubDataHomoloGene | Functions to download public domain annotation data sources |
getPubDataKegg | Functions to download public domain annotation data sources |
getPubDataLocusLink | Functions to download public domain annotation data sources |
getPubDataUniGene | Functions to download public domain annotation data sources |
getPubDataYeastGenome | Functions to download public domain annotation data sources |
getRatChrLengths | Functions that support a single API for building data packages |
getRefBuilt4HS | Functions that get the built date or number of the source data used for annotation |
getRefSeqBuilt | Functions that get the built date or number of the source data used for annotation |
getRefSeqUrl | Functions that find the correct url for downloading annotation data |
getRepList | Functions to build a data package using GO data |
getRepList4Perl | Supporting function that may no of any other usese |
getRepSourceNBuilt | Supporting function that may no of any other usese |
getReverseMapping | A function that maps LocusLink ids to other public repository ids and vice versa |
getShortSciName | Functions that produce short versions of organism names used by UniGene or for other purposes |
getSrcBuilt | Functions that get the built date or number of the source data used for annotation |
getSrcBuiltNRef | Functions that write supporting files needed by a data package |
getSrcNBuilt | Functions that write supporting files needed by a data package |
getSrcObjs | Supporting function that may no of any other usese |
getSrcObjs4Ath | Functions that build annotation packages for Arbidopsis |
getSrcUrl | Functions that find the correct url for downloading annotation data |
getStrand | Class "GP" a sub-class of pubRepo to get/process data from GoldenPath |
getStrand,GP-method | Class "GP" a sub-class of pubRepo to get/process data from GoldenPath |
getTaxid | Supporting function that may no of any other usese |
getTypeColNames | Functions that support a single API for building data packages |
getUCSCBuilt | Functions that get the built date or number of the source data used for annotation |
getUCSCUrl | Functions that find the correct url for downloading annotation data |
getUGBuilt | Functions that get the built date or number of the source data used for annotation |
getUGShortName | Functions that produce short versions of organism names used by UniGene or for other purposes |
getUGUrl | Functions that find the correct url for downloading annotation data |
getUniColNames | Functions that support a single API for building data packages |
getUnified | Functions to obtain unified mappings for a given set of ids using various sources |
getUniMappings | Supporting function that may no of any other usese |
getUrlNBuilt | Functions that write supporting files needed by a data package |
getVote | Functions to obtain unified mappings for a given set of ids using various sources |
getYeastChrLengths | Functions that support a single API for building data packages |
getYeastData | Functions to get/process yeast genome data |
getYGBuilt | Functions that get the built date or number of the source data used for annotation |
getYGExons | Functions to annotate yeast genom data |
getYGUrl | Functions that find the correct url for downloading annotation data |
GO | Class "GO" a class to handle data from Gene Ontology |
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 "GP" a sub-class of pubRepo to get/process data from GoldenPath |
GP-class | Class "GP" a sub-class of pubRepo to get/process data from GoldenPath |
gpLinkNGene | Functions to extract data from Golden Path |
hasDelimit | Functions to obtain unified mappings for a given set of ids using various sources |
HG | Class "HG" a class to represent HomoloGene data source |
HG-class | Class "HG" a class to represent HomoloGene data source |
HomoData2List | Functions to build a homology data package using data from NCBI |
homoPkgBuilder | Functions to build a homology data package using data from NCBI |
homoXMLParser | Functions to parse HomoloGene XML data file and build the homology annotation data package |
IPI | Class "IPI" a sub-class of pubRepo to handle data from International Protein Index (IPI) |
IPI-class | Class "IPI" a sub-class of pubRepo to handle data from International Protein Index (IPI) |
isOneToOne | A function to build a data pckage using Swiss-Prot protein data |
KEGG | Class "KEGG" a sub-class of pubRepo to get/process pathway and enzyme information |
KEGG,KEGG-method | Class "KEGG" a sub-class of pubRepo to get/process pathway and enzyme information |
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 |
key | A function to build a data pckage using Swiss-Prot protein data |
LL | Class "LL" a sub-class of pubRepo to handle data from LocusLink |
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 |
mapGO2Probe | Supporting function that may no of any other usese |
mapIntID | Functions to build a homology data package using data from NCBI |
mapll2EC | Functions to get/process pathway and enzyme data from KEGG |
mapLL2ECNPName | Class "KEGG" a sub-class of pubRepo to get/process pathway and enzyme information |
mapLL2ECNPName,KEGG-method | Class "KEGG" a sub-class of pubRepo to get/process pathway and enzyme information |
mapll2PathID | Supporting function that may no of any other usese |
mapLLNGB | Supporting function that may no of any other usese |
mapOrgs | Functions to build a homology data package using data from NCBI |
mapPS | Functions to build a homology data package using data from NCBI |
mapUGNGB | Supporting function that may no of any other usese |
matchAll | Creates a environment object using data from two columns of a matrix |
matchOneRow | Creates a environment object using data from two columns of a matrix |
matchProbes | Functions to read in the statistics about a data package |
mergeDupMatByFirstCol | Functions that build annotation packages for Arbidopsis |
mergeRowByKey | Dynamically create a Perl script to parse a source file base on user specifications |
MeSHParser | Function to parse the XML data file form MeSH |
nameGOByCat | Functions that support a single API for building data packages |
orgName | Class "UG" a sub-class of pubRepo to handle data from UniGene |
orgName,UG-method | Class "UG" a sub-class of pubRepo to handle data from UniGene |
orgName<-,UG-method | Class "UG" a sub-class of pubRepo to handle data from UniGene |
orgNameNCode | Functions to build a homology data package using data from NCBI |
parseData | Class "pubRepo" a generic class for downloading/parsing data provided by various public data repositories |
parseData,EG-method | Class "EG" handles data provided by Entrez Gene |
parseData,IPI-method | Class "IPI" a sub-class of pubRepo to handle data from International Protein Index (IPI) |
parseData,pubRepo-method | Class "pubRepo" a generic class for downloading/parsing data provided by various public data repositories |
parseEC | Functions to get/process pathway and enzyme data from KEGG |
parseKEGGGenome | Class "KEGG" a sub-class of pubRepo to get/process pathway and enzyme information |
parser | Class "pubRepo" a generic class for downloading/parsing data provided by various public data repositories |
parser,pubRepo-method | Class "pubRepo" a generic class for downloading/parsing data provided by various public data repositories |
parser<-,pubRepo-method | Class "pubRepo" a generic class for downloading/parsing data provided by various public data repositories |
print.ABQCList | Prints the quality control results for a given data package in a nice format |
procHomoData | Functions to build a homology data package using data from NCBI |
procPMIDData | Functions that build annotation packages for Arbidopsis |
procYeastGeno | Functions to annotate yeast genom data |
pubDataURLs | Public Domain Data Source URLs |
pubRepo | Class "pubRepo" a generic class for downloading/parsing data provided by various public data repositories |
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 |
readAthData | Functions that build annotation packages for Arbidopsis |
readBadData | Functions to get/process yeast genome data |
readData | Class "pubRepo" a generic class for downloading/parsing data provided by various public data repositories |
readData,GEO-method | Class "GEO" represents a GEO object that reads/downloads data from the GEO web site |
readData,GO-method | Class "GO" a class to handle data from Gene Ontology |
readData,HG-method | Class "HG" a class to represent HomoloGene data source |
readData,pubRepo-method | Class "pubRepo" a generic class for downloading/parsing data provided by various public data repositories |
readData,YG-method | Class "YG" a sub-class of pubRepo that reads/downloads data from yeast genomic |
readSourceUrlConfig | Read a data source URL config file |
readURL | Functions that find the correct url for downloading annotation data |
resolveMaps | Functions to obtain unified mappings for a given set of ids using various sources |
resumeSrcUrl | Functions that support a single API for building data packages |
reverseMap4GO | A function that maps LocusLink ids to other public repository ids and vice versa |
saveColSepData | A function that maps LocusLink ids to other public repository ids and vice versa |
saveCytoband | A function to build a data package containing mappings between LocusLink ids and the chromosomal locations of genes represented by the LocusLink ids |
saveData2Env | A function that maps LocusLink ids to other public repository ids and vice versa |
saveList | Functions that support a single API for building data packages |
saveMat | Functions that support a single API for building data packages |
saveOrgNameNCode | Functions to build a homology data package using data from NCBI |
sealEnvs | Functions to add namespaces for data files or seal the environment objects in the data subdirectory |
setVars | Function to parse the XML data file form MeSH |
sourceURLs | A data file contains urls for data available from various public repositories |
splitEntry | Functions that support a single API for building data packages |
SPPkgBuilder | A function to build a data pckage using Swiss-Prot protein data |
srcUrl | Class "pubRepo" a generic class for downloading/parsing data provided by various public data repositories |
srcUrl,pubRepo-method | Class "pubRepo" a generic class for downloading/parsing data provided by various public data repositories |
srcUrl<-,pubRepo-method | Class "pubRepo" a generic class for downloading/parsing data provided by various public data repositories |
twoStepSplit | Functions that support a single API for building data packages |
UG | Class "UG" a sub-class of pubRepo to handle data from UniGene |
UG-class | Class "UG" a sub-class of pubRepo to handle data from UniGene |
UGSciNames | Functions that produce short versions of organism names used by UniGene or for other purposes |
unifyMappings | A function to unify mapping result from different sources |
unzipFile | Functions to load files from a web site |
validateUrl | Functions to load files from a web site |
vect2List | Functions that support a single API for building data packages |
wget | Wrapper for system wget |
writeAccessory | Functions that write supporting files needed by a data package |
writeAnnData2Pkg | Supporting function that may no of any other usese |
writeChrLength | Functions that creates binary files for chromosome length and organism |
writeDatalist | Functions that support a single API for building data packages |
writeDescription | Functions that write supporting files needed by a data package |
writeDocs | Functions to build a data package using GO data |
writeFun | Functions that write supporting files needed by a data package |
writeHGID2Caption | Functions to parse HomoloGene XML data file and build the homology annotation data package |
writeHGID2LL | Functions to parse HomoloGene XML data file and build the homology annotation data package |
writeHomoData | Functions to parse HomoloGene XML data file and build the homology annotation data package |
writeHomoXMLData | Functions to parse HomoloGene XML data file and build the homology annotation data package |
writeMan4Fun | Functions that write supporting files needed by a data package |
writeMan4QC | Functions that write supporting files needed by a data package |
writeManPage | Functions that write supporting files needed by a data package |
writeOrganism | Functions that creates binary files for chromosome length and organism |
writeRdaNMan | Functions to build a homology data package using data from NCBI |
writeREADME | Functions that write supporting files needed by a data package |
writeReverseMap | Supporting function that may no of any other usese |
writeSourceUrlConfig | Create a source URL config file |
writeXMLHeader | A function to write header information to an XML file. |
writeZZZ | Functions that write supporting files needed by a data package |
yeastAnn | Functions to annotate yeast genom data |
yeastPkgBuilder | Functions to do a data package for yeast genome |
YG | Class "YG" a sub-class of pubRepo that reads/downloads data from yeast genomic |
YG-class | Class "YG" a sub-class of pubRepo that reads/downloads data from yeast genomic |