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

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("ENVISIONQuery")
AuthorAlex Lisovich, Roger Day
Bioconductor views Annotation
Date of publicationNone
MaintainerAlex Lisovich <all67@pitt.edu>, Roger Day <day01@pitt.edu>
LicenseGPL-2
Version1.24.0

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.

Functions

ENVISIONQuery Man page
ENVISIONQuery.chunk Man page
ENVISIONQuery.loop Man page
ENVISIONQuery-package Man page
ENVISIONServices Man page
formatIdMap Man page
formatIntact Man page
formatPicr Man page
formatReactome Man page
getFormatter Man page
getIdEntries Man page
getIdMatchInfo Man page
getInputIdEntries Man page
getInputTypes Man page
getIntactMatchInfo Man page
getMerger Man page
getPicrMatchInfo Man page
getPositiveResultSetIDs Man page
getReactomeMatchInfo Man page
getService Man page
getServiceClient Man page
getServiceNames Man page
getServiceOptions Man page
getServices Man page
getTool Man page
getToolNames Man page
jgetOptions Man page
mergeFrameList Man page
mergeMatchRows Man page
progressMsg Man page
registerServices Man page
toChunks Man page

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.