FlowRepositoryR: FlowRepository R Interface
Version 1.8.0

This package provides an interface to search and download data and annotations from FlowRepository (flowrepository.org). It uses the FlowRepository programming interface to communicate with a FlowRepository server.

AuthorJosef Spidlen [aut, cre]
Bioconductor views FlowCytometry Infrastructure
Date of publicationNone
MaintainerJosef Spidlen <jspidlen@gmail.com>
LicenseArtistic-2.0
Version1.8.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("FlowRepositoryR")

Getting started

Package overview

Popular man pages

attachmentProxy-class: 'attachmentProxy': a class representing a proxy to an...
download-methods: Download dataset files
FlowRepositoryR-package: Programming interface to access FlowRepository.org
ilarCodeDescription: Get the name of a lab from it's ILAR code
impcCodeDescription: Get a human readable description of an IMPC code.
impcResultsCopy-methods: Retrieve a copy of IMPC results associated with a flowRepData...
setFlowRepositoryCredentials: Set credentials (email and password) to login to...
See all...

All man pages Function index File listing

Man pages

attachmentProxy-class: 'attachmentProxy': a class representing a proxy to an...
download-methods: Download dataset files
fcsProxy-class: 'fcsProxy': a class representing a proxy to an FCS file in...
fileProxy-class: 'fileProxy': a class representing a proxy to a file in...
flowRepData-class: 'flowRepData': a class for storing metadata about a...
flowRep.get: Retrieve information about a specified FlowRepository...
flowRep.ls: List identifiers of datasets available in FlowRepository
flowRepOrganization-class: 'flowRepOrganization': a class for storing details about an...
FlowRepositoryR-package: Programming interface to access FlowRepository.org
flowRep.search: Search FlowRepository for datasets matching the query and...
flowRep.submitGeneStatus: Submit information about an IMPC gene analysis results to...
flowRep.submitImpcResults: Submit IMPC data analysis results to FlowRepository.
forgetFlowRepositoryCredentials: Forgets credentials (email and password) to login to...
getFlowRepositoryURL: Get FlowRepository URL addresss.
id-methods: Retrieve the identifier of flowRepData objects
ilarCodeDescription: Get the name of a lab from it's ILAR code
impcCodeDescription: Get a human readable description of an IMPC code.
impcResultsCopy-methods: Retrieve a copy of IMPC results associated with a flowRepData...
is.downloaded-methods: Check if a dataset or a file proxy is downloaded
listKnownIlarCodes: List all known ILAR codes.
setFlowRepositoryCredentials: Set credentials (email and password) to login to...
setFlowRepositoryURL: Set FlowRepository URL addresss.

Functions

FlowRepositoryR Man page
FlowRepositoryR-package Man page
attachmentProxy Man page Source code
attachmentProxy-class Man page
attachments Man page
attachments,flowRepData,attachments-method Man page
attachments,flowRepData-method Man page
attachments<- Man page
attachments<-,flowRepData-method Man page
download Man page
download,attachmentProxy-method Man page
download,fcsProxy-method Man page
download,fileProxy,download-method Man page
download,fileProxy-method Man page
download,flowRepData,download-method Man page
download,flowRepData-method Man page
extractAttachmentsInfo Source code
extractFCSFilesInfo Source code
extractImpcInfo Source code
extractKeywords Source code
extractOrganizations Source code
extractPublications Source code
fcs.files Man page
fcs.files,flowRepData,fcs.files-method Man page
fcs.files,flowRepData-method Man page
fcs.files<- Man page
fcs.files<-,flowRepData-method Man page
fcsProxy Man page Source code
fcsProxy-class Man page
fileProxy Man page
fileProxy-class Man page
flowRep.get Man page Source code
flowRep.login Source code
flowRep.logout Source code
flowRep.ls Man page Source code
flowRep.search Man page Source code
flowRep.submitGeneStatus Man page Source code
flowRep.submitImpcResults Man page Source code
flowRepData Man page Source code
flowRepData-class Man page
flowRepOrganization Man page Source code
flowRepOrganization-class Man page
forgetFlowRepositoryCredentials Man page Source code
getElValAsChar Source code
getElValAsLogicle Source code
getElValAsNum Source code
getFlowRepositoryClientID Source code
getFlowRepositoryCredentials Source code
getFlowRepositoryURL Man page Source code
haveFlowRepositoryCredentials Source code
id Man page
id,flowRepData,id-method Man page
id,flowRepData-method Man page
ilarCodeDescription Man page Source code
impc.experiments Man page
impc.experiments,flowRepData,impc.experiments-method Man page
impc.experiments,flowRepData-method Man page
impc.experiments<- Man page
impc.experiments<-,flowRepData-method Man page
impcCodeDescription Man page Source code
impcResultsCopy Man page
impcResultsCopy,flowRepData,impcResultsCopy-method Man page
impcResultsCopy,flowRepData-method Man page
is.downloaded Man page
is.downloaded,attachmentProxy-method Man page
is.downloaded,fcsProxy-method Man page
is.downloaded,fileProxy,is.downloaded-method Man page
is.downloaded,fileProxy-method Man page
is.downloaded,flowRepData,is.downloaded-method Man page
is.downloaded,flowRepData-method Man page
listKnownIlarCodes Man page Source code
localpath Man page
localpath,fileProxy,localpath-method Man page
localpath,fileProxy-method Man page
organizations Man page
organizations,flowRepData,organizations-method Man page
organizations,flowRepData-method Man page
preprocessHttpHeader Source code
setFlowRepositoryCredentials Man page Source code
setFlowRepositoryURL Man page Source code
smartTreeParse Source code
summary,attachmentProxy-method Man page
summary,fcsProxy-method Man page
summary,fileProxy-method Man page
summary,flowRepData-method Man page
summary,flowRepOrganization-method Man page

Files

DESCRIPTION
NAMESPACE
R
R/AllClasses.R
R/accessor-methods.R
R/exported-functions.R
R/helper-functions.R
R/methods.R
R/parsing-methods.R
R/settings.R
R/summary-methods.R
build
build/vignette.rds
inst
inst/NEWS
inst/doc
inst/doc/HowTo-FlowRepositoryR.R
inst/doc/HowTo-FlowRepositoryR.Rnw
inst/doc/HowTo-FlowRepositoryR.pdf
inst/unitTests
inst/unitTests/test_downloads.R
inst/unitTests/test_flowRep.get.R
inst/unitTests/test_flowRep.ls.R
inst/unitTests/test_flowRep.search.R
inst/unitTests/test_generics.R
inst/unitTests/test_helpers.R
inst/unitTests/test_impc_dict.R
inst/unitTests/test_settings.R
man
man/FlowRepositoryR-package.Rd
man/attachmentProxy-class.Rd
man/download-methods.Rd
man/fcsProxy-class.Rd
man/fileProxy-class.Rd
man/flowRep.get.Rd
man/flowRep.ls.Rd
man/flowRep.search.Rd
man/flowRep.submitGeneStatus.Rd
man/flowRep.submitImpcResults.Rd
man/flowRepData-class.Rd
man/flowRepOrganization-class.Rd
man/forgetFlowRepositoryCredentials.Rd
man/getFlowRepositoryURL.Rd
man/id-methods.Rd
man/ilarCodeDescription.Rd
man/impcCodeDescription.Rd
man/impcResultsCopy-methods.Rd
man/is.downloaded-methods.Rd
man/listKnownIlarCodes.Rd
man/setFlowRepositoryCredentials.Rd
man/setFlowRepositoryURL.Rd
tests
tests/runTests.R
vignettes
vignettes/FlowRepositorySetAPIpasswd.png
vignettes/HowTo-FlowRepositoryR.Rnw
vignettes/Refs.bib
FlowRepositoryR documentation built on May 20, 2017, 9:33 p.m.

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