Package: BaseSpaceR 1.51.0

Jared OConnell

BaseSpaceR: R SDK for BaseSpace RESTful API

A rich R interface to Illumina's BaseSpace cloud computing environment, enabling the fast development of data analysis and visualisation tools.

Authors:Adrian Alexa

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BaseSpaceR/json (API)
NEWS

# Install 'BaseSpaceR' in R:

install.packages('BaseSpaceR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

aAuth - Sample 'AppAuth' instance with 'browse global' scope

On BioConductor:BaseSpaceR-1.49.0(bioc 3.20)BaseSpaceR-1.48.0(bioc 3.19)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

infrastructure datarepresentation connecttools software dataimport highthroughputsequencing sequencing genetics

3.30 score 9 scripts 312 downloads 73 exports 3 dependencies

Last updated 23 days agofrom:835c641988. Checks:OK: 1 WARNING: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 30 2024
R-4.5-win	WARNING	Oct 30 2024
R-4.5-linux	WARNING	Oct 30 2024
R-4.4-win	WARNING	Oct 30 2024
R-4.4-mac	WARNING	Oct 30 2024
R-4.3-win	WARNING	Oct 30 2024
R-4.3-mac	WARNING	Oct 30 2024

Exports:AppAuth appResultCollection appResultItem AppResults AppSessions as.list auth authNativeClient authWebClient countAppResults countAppSessions countFiles countGenomes countProjects countRuns countSamples createAppResults createProject DateCreated DisplayedCount fileCollection fileItem Files genomeCollection genomeItem Genomes getBAMs getCoverage getCoverageStats getFiles getIndexedBam getVariants getVariantSet hasAccess Href HrefBaseSpaceUI Id initializeAuth Items Limit listAppResults listAppSessions listFiles listGenomes listProjects listRuns listSamples Name Offset performOAuth projectCollection projectItem Projects putFiles requestAccessToken ResponseStatus runCollection runItem Runs sampleCollection sampleItem Samples ServiceURI show SortBy SortDir Status TotalCount updateAppSessions uri userItem UserOwnedBy Users

Dependencies:bitops RCurl RJSONIO

BaseSpaceR

Rendered fromBaseSpaceR.Rnwusingutils::Sweaveon Oct 30 2024.

Last update: 2018-08-28
Started: 2013-11-01

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
R SDK for BaseSpace RESTful API	BaseSpaceR-package BaseSpaceR
Sample 'AppAuth' instance with 'browse global' scope	aAuth
'AppAuth' class	AppAuth AppAuth-class hasAccess hasAccess,AppAuth-method initializeAuth initializeAuth,AppAuth-method performOAuth requestAccessToken requestAccessToken,AppAuth-method
'AppResults' and '"AppResultsSummary"' objects	appResultCollection appResultCollection-class appResultItem appResultItem-class AppResults AppResults,AppAuth-method AppResults,AppResultsSummary-method AppResults,missing-method AppResults-class AppResultsSummary-class countAppResults countAppResults,AppAuth-method countAppResults,Projects-method countAppResults,ProjectsSummary-method countAppResults,Response-method createAppResults createAppResults,AppAuth-method createAppResults,Projects-method listAppResults listAppResults,AppAuth-method listAppResults,Projects-method
'AppSessionAuth' class	AppSessionAuth-class authNativeClient authWebClient
'AppSessions' object	appSessionItem appSessionItem-class AppSessions AppSessions,AppAuth-method AppSessions,AppResults-method AppSessions-class countAppSessions countAppSessions,AppAuth-method countAppSessions,Response-method listAppSessions listAppSessions,AppAuth-method updateAppSessions updateAppSessions,AppAuth-method
Methods for accessing coverage data from BAM files	getCoverage getCoverage,AppAuth-method getCoverageStats getCoverageStats,AppAuth-method
'Files' and 'FilesSummary' objects	countFiles countFiles,AppAuth-method countFiles,AppResults-method countFiles,AppResultsSummary-method countFiles,Response-method countFiles,Runs-method countFiles,RunsSummary-method countFiles,Samples-method countFiles,SamplesSummary-method fileCollection fileCollection-class fileItem fileItem-class Files Files,AppAuth-method Files,FilesSummary-method Files,missing-method Files-class FilesSummary-class getFiles getFiles,AppAuth-method listFiles listFiles,AppAuth-method listFiles,AppResults-method listFiles,AppResultsSummary-method listFiles,Runs-method listFiles,RunsSummary-method listFiles,Samples-method listFiles,SamplesSummary-method putFiles putFiles,AppAuth-method
High-level methods for 'Files' objects and related	getBAMs getBAMs,AppResults-method getIndexedBam
'Genomes' and 'GenomesSummary' objects	countGenomes genomeCollection genomeCollection-class genomeItem genomeItem-class Genomes Genomes,AppAuth-method Genomes,GenomesSummary-method Genomes,missing-method Genomes-class GenomesSummary-class listGenomes listGenomes,AppAuth-method listGenomes,Response-method
Internal methods	as.character,staticHref-method auth,Href-method show,Href-method show,staticHref-method
'Projects' and 'ProjectsSummary' objects	countProjects countProjects,AppAuth-method countProjects,Response-method createProject createProject,AppAuth-method listProjects listProjects,AppAuth-method listProjects,Response-method projectCollection projectCollection-class projectItem projectItem-class Projects Projects,AppAuth-method Projects,missing-method Projects,ProjectsSummary-method Projects-class ProjectsSummary-class
'Item', 'Collection' and 'Response' objects	$,Collection-method $,Item-method $,Response-method as.list,Collection-method as.list,Item-method as.list,Response-method auth auth,Response-method Collection-class DateCreated DateCreated,Collection-method DateCreated,Item-method DateCreated,Response-method DisplayedCount DisplayedCount,Collection-method DisplayedCount,Item-method DisplayedCount,Response-method Href Href,Collection-method Href,Item-method Href,Response-method HrefBaseSpaceUI HrefBaseSpaceUI,Collection-method HrefBaseSpaceUI,Item-method HrefBaseSpaceUI,Response-method Id Id,Collection-method Id,Item-method Id,Response-method Item-class Items Items,Collection-method Items,Item-method Items,Response-method length,Collection-method length,Item-method length,Response-method Limit Limit,Collection-method Limit,Item-method Limit,Response-method Name Name,Collection-method Name,Item-method Name,Response-method Offset Offset,Collection-method Offset,Item-method Offset,Response-method Response-class show,Collection-method show,Item-method show,Response-method SortBy SortBy,Collection-method SortBy,Item-method SortBy,Response-method SortDir SortDir,Collection-method SortDir,Item-method SortDir,Response-method Status Status,Collection-method Status,Item-method Status,Response-method TotalCount TotalCount,Collection-method TotalCount,Item-method TotalCount,Response-method UserOwnedBy UserOwnedBy,Collection-method UserOwnedBy,Item-method UserOwnedBy,Response-method [,Collection-method [,Response-method [[,Collection,numeric-method [[,Response,ANY-method
Class '"ResponseStatus"'	ResponseStatus ResponseStatus-class show,ResponseStatus-method
'Runs' and 'RunsSummary' objects	countRuns countRuns,AppAuth-method countRuns,Response-method listRuns listRuns,AppAuth-method listRuns,Response-method runCollection runCollection-class runItem runItem-class Runs Runs,AppAuth-method Runs,missing-method Runs,RunsSummary-method Runs-class RunsSummary-class
'Samples' and 'SamplesSummary' objects	countSamples countSamples,AppAuth-method countSamples,Projects-method countSamples,ProjectsSummary-method countSamples,Response-method listSamples listSamples,AppAuth-method listSamples,Projects-method sampleCollection sampleCollection-class sampleItem sampleItem-class Samples Samples,AppAuth-method Samples,missing-method Samples,SamplesSummary-method Samples-class SamplesSummary-class
Class '"ServiceURI"'	ServiceURI ServiceURI-class show,ServiceURI-method uri uri,ServiceURI-method
'Users' objects and resources	userItem userItem-class Users Users,AppAuth-method Users,missing-method Users,Response-method Users-class
Methods for accessing varinant data	getVariants getVariants,AppAuth-method getVariantSet getVariantSet,AppAuth-method