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

AuthorAlex Lisovich, Roger Day
Date of publicationNone
MaintainerAlex Lisovich <all67@pitt.edu>, Roger Day <day01@pitt.edu>
LicenseGPL-2
Version1.22.0

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

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