ABPkgBuilder	ABPkgBuilder
addNamespace	addNamespace
athPkgBuilder	athPkgBuilder
baseFile	pubRepo-class
baseFile,pubRepo-method	pubRepo-class
baseFile<-	pubRepo-class
baseFile<-,pubRepo-method	pubRepo-class
builtInfo	pubRepo-class
builtInfo,pubRepo-method	pubRepo-class
chrLocPkgBuilder	chrLocPkgBuilder
cleanSrcObjs	cleanSrcObjs
cMAPParser	cMapPathBuilder
cMapPathBuilder	cMapPathBuilder
cols2Env	cols2Env
copyTemplates	GOPkgBuilder
countMapping	getDPStats
createEmptyDPkg	ABPkgBuilder
downloadData	pubRepo-class
downloadData,pubRepo-method	pubRepo-class
downloadSourceData	downloadSourceData
EG	EG-class
EG-class	EG-class
escapeLatexChr	writeManPage
fileMuncher	fileMuncher
fileToXML	fileToXML
findChrLength	writeChrLength
findIDNPath	KEGG-class
findIDNPath,KEGG-method	KEGG-class
findNumCol	getYeastData
findYGChrLength	yeastPkgBuilder
formatABQCList	getDPStats
formatChrLoc	yeastAnn
formatGO	yeastAnn
formatName	writeManPage
fromWeb	pubRepo-class
fromWeb,pubRepo-method	pubRepo-class
fromWeb<-	pubRepo-class
fromWeb<-,pubRepo-method	pubRepo-class
GEO	GEO-class
GEO-class	GEO-class
getAllRdaName	writeManPage
getAllSrc	makeSrcInfo
getAllUrl	getSrcUrl
getAnnData	cleanSrcObjs
getBaseFile	cleanSrcObjs
getBaseParsers	ABPkgBuilder
getBuild4Yeast	writeManPage
getChrLenghts	ABPkgBuilder
getChrLengths	ABPkgBuilder
getChrNum	chrLocPkgBuilder
getChroLocation	getChroLocation
getChroms4Org	chrLocPkgBuilder
getCytoList	getChroLocation
getCytoLoc	getChroLocation
getDate	getDPStats
getDetailV	SPPkgBuilder
getDirContent	ABPkgBuilder
getDPStats	getDPStats
getDSrc	writeManPage
getDsrc	writeManPage
getEGAccName	ABPkgBuilder
getEGBuilt	getSrcBuilt
getEGUrl	getSrcUrl
getEIdNName	KEGGPkgBuilder
getEnvNames	SPPkgBuilder
getExample	writeManPage
getExten	map2LL
getGEOUrl	getSrcUrl
getGEOYeast	yeastAnn
getGOBuilt	getSrcBuilt
getGOUrl	getSrcUrl
getGPData	getChroLocation
getHGBuilt	getSrcBuilt
getHGUrl	getSrcUrl
getHomoData	homoPkgBuilder
getHomoDList	homoPkgBuilder
getHomoPS	homoPkgBuilder
getHumanChrLengths	ABPkgBuilder
getIntIDMapping	homoPkgBuilder
getItem	writeManPage
getKEGGBuilt	getSrcBuilt
getKEGGFile	KEGGPkgBuilder
getKEGGGeneMap	KEGGPkgBuilder
getKEGGIDNName	getKEGGIDNName
getKEGGOrgName	getKEGGIDNName
getKEGGUrl	getSrcUrl
getList4GO	ABPkgBuilder
getLL2ACC	map2LL
getLL2IntID	homoPkgBuilder
getLLBuilt	getSrcBuilt
getLLNGBMap	cleanSrcObjs
getLLPathMap	getKEGGIDNName
getLLUrl	getSrcUrl
getMouseChrLengths	ABPkgBuilder
getMultiColNames	ABPkgBuilder
getNoDup	resolveMaps
getOneMap	athPkgBuilder
getOrgName	map2LL
getOrgNameNCode	homoPkgBuilder
getPBased	getDPStats
getProbe2SGD	yeastAnn
getProbeNum	getDPStats
getPubDataEntrezGene	getPubDataGo
getPubDataGo	getPubDataGo
getPubDataGoldenPath	getPubDataGo
getPubDataHomoloGene	getPubDataGo
getPubDataKegg	getPubDataGo
getPubDataLocusLink	getPubDataGo
getPubDataUniGene	getPubDataGo
getPubDataYeastGenome	getPubDataGo
getRatChrLengths	ABPkgBuilder
getRefBuilt4HS	getSrcBuilt
getRefSeqBuilt	getSrcBuilt
getRefSeqUrl	getSrcUrl
getRepList	GOPkgBuilder
getRepList4Perl	cleanSrcObjs
getRepSourceNBuilt	cleanSrcObjs
getReverseMapping	map2LL
getShortSciName	getUGShortName
getSrcBuilt	getSrcBuilt
getSrcBuiltNRef	writeManPage
getSrcNBuilt	writeManPage
getSrcObjs	cleanSrcObjs
getSrcObjs4Ath	athPkgBuilder
getSrcUrl	getSrcUrl
getStrand	GP-class
getStrand,GP-method	GP-class
getTaxid	cleanSrcObjs
getTypeColNames	ABPkgBuilder
getUCSCBuilt	getSrcBuilt
getUCSCUrl	getSrcUrl
getUGBuilt	getSrcBuilt
getUGShortName	getUGShortName
getUGUrl	getSrcUrl
getUniColNames	ABPkgBuilder
getUnified	resolveMaps
getUniMappings	cleanSrcObjs
getUrlNBuilt	writeManPage
getVote	resolveMaps
getYeastChrLengths	ABPkgBuilder
getYeastData	getYeastData
getYGBuilt	getSrcBuilt
getYGExons	yeastAnn
getYGUrl	getSrcUrl
GO	GO-class
GO-class	GO-class
GOPkgBuilder	GOPkgBuilder
GOXMLParser	GOXMLParser
GP	GP-class
GP-class	GP-class
gpLinkNGene	getChroLocation
hasDelimit	resolveMaps
HG	HG-class
HG-class	HG-class
HomoData2List	homoPkgBuilder
homoPkgBuilder	homoPkgBuilder
homoXMLParser	writeHomoXMLData
isOneToOne	SPPkgBuilder
KEGG	KEGG-class
KEGG,KEGG-method	KEGG-class
KEGG-class	KEGG-class
KEGGPkgBuilder	KEGGPkgBuilder
key	SPPkgBuilder
LL	LL-class
LL-class	LL-class
loadFromUrl	loadFromUrl
makeLLDB	makeLLDB
makeSrcInfo	makeSrcInfo
map2LL	map2LL
mapGO2Probe	cleanSrcObjs
mapIntID	homoPkgBuilder
mapll2EC	getKEGGIDNName
mapLL2ECNPName	KEGG-class
mapLL2ECNPName,KEGG-method	KEGG-class
mapll2PathID	cleanSrcObjs
mapLLNGB	cleanSrcObjs
mapOrgs	homoPkgBuilder
mapPS	homoPkgBuilder
mapUGNGB	cleanSrcObjs
matchAll	cols2Env
matchOneRow	cols2Env
matchProbes	getDPStats
mergeDupMatByFirstCol	athPkgBuilder
mergeRowByKey	fileMuncher
MeSHParser	MeSHParser
nameGOByCat	ABPkgBuilder
orgName	UG-class
orgName,UG-method	UG-class
orgName<-	UG-class
orgName<-,UG-method	UG-class
orgNameNCode	homoPkgBuilder
parseData	pubRepo-class
parseData,EG-method	EG-class
parseData,pubRepo-method	pubRepo-class
parseEC	getKEGGIDNName
parseKEGGGenome	KEGG-class
parser	pubRepo-class
parser,pubRepo-method	pubRepo-class
parser<-	pubRepo-class
parser<-,pubRepo-method	pubRepo-class
print.ABQCList	print.ABQCList
procHomoData	homoPkgBuilder
procPMIDData	athPkgBuilder
procYeastGeno	yeastAnn
pubDataURLs	pubDataURLs
pubRepo	pubRepo-class
pubRepo-class	pubRepo-class
queryGEO	queryGEO
readAthData	athPkgBuilder
readBadData	getYeastData
readData	pubRepo-class
readData,GEO-method	GEO-class
readData,GO-method	GO-class
readData,HG-method	HG-class
readData,pubRepo-method	pubRepo-class
readData,YG-method	YG-class
readSourceUrlConfig	readSourceUrlConfig
readURL	getSrcUrl
resolveMaps	resolveMaps
resumeSrcUrl	ABPkgBuilder
reverseMap4GO	map2LL
saveColSepData	map2LL
saveCytoband	chrLocPkgBuilder
saveData2Env	map2LL
saveList	ABPkgBuilder
saveMat	ABPkgBuilder
saveOrgNameNCode	homoPkgBuilder
sealEnvs	addNamespace
setVars	MeSHParser
sourceURLs	sourceURLs
splitEntry	ABPkgBuilder
SPPkgBuilder	SPPkgBuilder
srcUrl	pubRepo-class
srcUrl,pubRepo-method	pubRepo-class
srcUrl<-	pubRepo-class
srcUrl<-,pubRepo-method	pubRepo-class
twoStepSplit	ABPkgBuilder
UG	UG-class
UG-class	UG-class
UGSciNames	getUGShortName
unifyMappings	unifyMappings
unzipFile	loadFromUrl
validateUrl	loadFromUrl
vect2List	ABPkgBuilder
wget	wget
writeAccessory	writeManPage
writeAnnData2Pkg	cleanSrcObjs
writeChrLength	writeChrLength
writeDatalist	ABPkgBuilder
writeDescription	writeManPage
writeDocs	GOPkgBuilder
writeFun	writeManPage
writeHGID2Caption	writeHomoXMLData
writeHGID2LL	writeHomoXMLData
writeHomoData	writeHomoXMLData
writeHomoXMLData	writeHomoXMLData
writeMan4Fun	writeManPage
writeMan4QC	writeManPage
writeManPage	writeManPage
writeOrganism	writeChrLength
writeRdaNMan	homoPkgBuilder
writeREADME	writeManPage
writeReverseMap	cleanSrcObjs
writeSourceUrlConfig	writeSourceUrlConfig
writeXMLHeader	writeXMLHeader
writeZZZ	writeManPage
yeastAnn	yeastAnn
yeastPkgBuilder	yeastPkgBuilder
YG	YG-class
YG-class	YG-class
