ENVISIONQuery: Retrieval from the ENVISION bioinformatics data portal into R

Tools to retrieve data from ENVISION, the Database for Annotation, Visualization and Integrated Discovery portal

Author
Alex Lisovich, Roger Day
Date of publication
None
Maintainer
Alex Lisovich <all67@pitt.edu>, Roger Day <day01@pitt.edu>
License
GPL-2
Version
1.22.0

View on Bioconductor

Man pages

ENVISIONQuery
Launch a query against Envision, a web online query system...
ENVISIONQuery.chunk
Retrieves a set of unique matches for a given ID list.
ENVISIONQuery.loop
Perform queries in chunks to comply with potential...
ENVISIONQuery-package
ENVISIONQuery.
ENVISIONServices
Registry of available Envision services...
formatIdMap
Convert the Enfin xml ID conversion results file into the...
formatIntact
Convert the EnXML IntAct service results file into the...
formatPicr
Convert the EnXML PICR service results file into the protein...
formatReactome
Convert the EnXML PICR service results file into the protein...
getFormatter
Get the formatting function for a given tool...
getIdEntries
Retrieve a set of all ID entries...
getIdMatchInfo
Retrieve the set of match pairs from the 'Entry' node of the...
getInputIdEntries
Retrieve a set of input ID entries...
getInputTypes
Get the list of available input types for a given tool.
getIntactMatchInfo
Retrieve IntAct match info from the 'Entry' node of the Enfin...
getMerger
Get the merging function for a given tool.
getPicrMatchInfo
Retrieve PICR match info from the 'Entry' node of the Enfin...
getPositiveResultSetIDs
Retrieve a set of positive query result references from the...
getReactomeMatchInfo
Retrieve Reactome pathway match info from the 'Entry' node of...
getService
Get the service handler using it's name...
getServiceClient
Get the Web Service client finction handler for a given...
getServiceNames
Get the names of available Envision services...
getServiceOptions
Get default service options.
getServices
Get available services...
getTool
Get the tool handler of a given service using the tool...
getToolNames
Get the names of available tools for a given Envision...
jgetOptions
Convert options list into the character vector.
mergeFrameList
Merges the data frames representing the partial query results...
mergeMatchRows
Merge a set of rows with non-unique values in a given set of...
progressMsg
Display the task progress message.
registerServices
Register available Envision services...
toChunks
Convert the ID set into the list of ID subsets.

Files in this package

ENVISIONQuery/.BBSoptions
ENVISIONQuery/DESCRIPTION
ENVISIONQuery/NAMESPACE
ENVISIONQuery/R
ENVISIONQuery/R/ENVISIONQuery-package.R
ENVISIONQuery/R/ENVISIONQuery.R
ENVISIONQuery/R/ENVISIONServices.R
ENVISIONQuery/R/formatEnXML.R
ENVISIONQuery/R/formatIdConversion.R
ENVISIONQuery/R/formatIntact.R
ENVISIONQuery/R/formatPicr.R
ENVISIONQuery/R/formatReactome.R
ENVISIONQuery/R/registerServices.R
ENVISIONQuery/R/zzz.R
ENVISIONQuery/build
ENVISIONQuery/build/vignette.rds
ENVISIONQuery/inst
ENVISIONQuery/inst/doc
ENVISIONQuery/inst/doc/ENVISIONQuery.R
ENVISIONQuery/inst/doc/ENVISIONQuery.Rnw
ENVISIONQuery/inst/doc/ENVISIONQuery.pdf
ENVISIONQuery/inst/jar
ENVISIONQuery/inst/jar/EnvisionQuery.jar
ENVISIONQuery/inst/jar/jaxws-tools-2.1.4.jar
ENVISIONQuery/man
ENVISIONQuery/man/ENVISIONQuery-package.Rd
ENVISIONQuery/man/ENVISIONQuery.Rd
ENVISIONQuery/man/ENVISIONQuery.chunk.Rd
ENVISIONQuery/man/ENVISIONQuery.loop.Rd
ENVISIONQuery/man/ENVISIONServices.Rd
ENVISIONQuery/man/formatIdMap.Rd
ENVISIONQuery/man/formatIntact.Rd
ENVISIONQuery/man/formatPicr.Rd
ENVISIONQuery/man/formatReactome.Rd
ENVISIONQuery/man/getFormatter.Rd
ENVISIONQuery/man/getIdEntries.Rd
ENVISIONQuery/man/getIdMatchInfo.Rd
ENVISIONQuery/man/getInputIdEntries.Rd
ENVISIONQuery/man/getInputTypes.Rd
ENVISIONQuery/man/getIntactMatchInfo.Rd
ENVISIONQuery/man/getMerger.Rd
ENVISIONQuery/man/getPicrMatchInfo.Rd
ENVISIONQuery/man/getPositiveResultSetIDs.Rd
ENVISIONQuery/man/getReactomeMatchInfo.Rd
ENVISIONQuery/man/getService.Rd
ENVISIONQuery/man/getServiceClient.Rd
ENVISIONQuery/man/getServiceNames.Rd
ENVISIONQuery/man/getServiceOptions.Rd
ENVISIONQuery/man/getServices.Rd
ENVISIONQuery/man/getTool.Rd
ENVISIONQuery/man/getToolNames.Rd
ENVISIONQuery/man/jgetOptions.Rd
ENVISIONQuery/man/mergeFrameList.Rd
ENVISIONQuery/man/mergeMatchRows.Rd
ENVISIONQuery/man/progressMsg.Rd
ENVISIONQuery/man/registerServices.Rd
ENVISIONQuery/man/toChunks.Rd
ENVISIONQuery/vignettes
ENVISIONQuery/vignettes/ENVISIONQuery.Rnw
ENVISIONQuery/vignettes/ENVISIONQuery.lyx