A B C D E F G H I K L M O P Q R S T U V W Y
ABPkgBuilder | Functions that support a single API for building data packages |
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 |
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 |
createEmptyDPkg | Functions that support a single API for building data packages |
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 |
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 | A function 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 |
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 |
getAncestors | Functions to read/parse the XML document of Gene Ontology data |
getBaseParsers | Functions that support a single API for building data packages |
getBuild4Yeast | Functions that write supporting files needed by a data package |
getChildNodes | Functions to read/parse the XML document of Gene Ontology data |
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 |
getDate | A function 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 | A function 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 |
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 |
getFullIDName | 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 |
getGOGroupIDs | Functions to read/parse the XML document of Gene Ontology data |
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 |
getHomoPS | Functions to build a homology data package using data from NCBI |
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 |
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 |
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 |
getLLPathMap | Functions to get/process pathway and enzyme data from KEGG |
getLLUrl | Functions that find the correct url for downloading annotation data |
getMultiColNames | Functions that support a single API for building data packages |
getNoDup | Functions to obtain unified mappings between ids |
getOffspringNodes | Functions to read/parse the XML document of Gene Ontology data |
getOrgName | A function that maps LocusLink ids to other public repository ids and vice versa |
getParentNodes | Functions to read/parse the XML document of Gene Ontology data |
getPBased | A function to read in the statistics about a data package |
getProbe2SGD | Functions to annotate yeast genom data |
getProbeNum | A function to read in the statistics about a data package |
getReverseMapping | A function that maps LocusLink ids to other public repository ids and vice versa |
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 |
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 |
getTopGOid | Functions to read/parse the XML document of Gene Ontology data |
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 |
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 between ids |
getUrl4Org | A function that maps LocusLink ids to other public repository ids and vice versa |
getUrlNBuilt | Functions that write supporting files needed by a data package |
getVote | Functions to obtain unified mappings between ids |
getYeastData | Functions to get/process yeast genome data |
getYGBuilt | Functions that get the built date or number of the source data used for annotation |
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 | A functions to builder a data package using GO data |
GOXMLParser | Functions to read/parse the XML document of Gene Ontology data |
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 between ids |
homoPkgBuilder | Functions to build a homology data package using data from NCBI |
homoPS-class | Class "homoPS" |
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 |
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 |
mapGO2AllProbe | Functions to read/parse the XML document of Gene Ontology data |
mapGO2Category | Functions to read/parse the XML document of Gene Ontology data |
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 |
mapOrgs | Functions to build a homology data package using data from NCBI |
mapPS | Functions to build a homology data package using data from NCBI |
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 | A function to read in the statistics about a data package |
mergeRowByKey | Dynamically create a Perl script to parse a source file base on user specifications |
organism | Class "UG" a sub-class of pubRepo to handle data from UniGene |
organism,UG-method | Class "UG" a sub-class of pubRepo to handle data from UniGene |
organism<-,UG-method | Class "UG" a sub-class of pubRepo to handle data from UniGene |
orgNameNCode | Class "homoPS" |
parseData | Class "pubRepo" a generic class for downloading/parsing data provided by various public data repositories |
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 |
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 |
procYeastGeno | Functions to annotate yeast genom data |
ps | Class "homoPS" |
ps,homoPS-method | Class "homoPS" |
psLL | Class "homoPS" |
psLL,homoPS-method | Class "homoPS" |
psOrg | Class "homoPS" |
psOrg,homoPS-method | Class "homoPS" |
psType | Class "homoPS" |
psType,homoPS-method | Class "homoPS" |
psURL | Class "homoPS" |
psURL,homoPS-method | Class "homoPS" |
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 |
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,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 |
readURL | Functions that find the correct url for downloading annotation data |
resolveMaps | Functions to obtain unified mappings between ids |
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 |
saveData2Env | A function that maps LocusLink ids to other public repository ids and vice versa |
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 |
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 |
writeAccessory | Functions that write supporting files needed by a data package |
writeChrLength | Functions that creates binary files for chromosome length and organism |
writeDescription | Functions that write supporting files needed by a data package |
writeFun | Functions that write supporting files needed by a 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 |
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 |