Package: BaseSpaceR 1.49.0
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:
BaseSpaceR_1.49.0.tar.gz
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BaseSpaceR.pdf |BaseSpaceR.html✨
BaseSpaceR/json (API)
NEWS
| # Install 'BaseSpaceR' in R: |
| install.packages('BaseSpaceR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
- 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.
Last updated 2 months agofrom:96bafdd0eb
Exports:AppAuthappResultCollectionappResultItemAppResultsAppSessionsas.listauthauthNativeClientauthWebClientcountAppResultscountAppSessionscountFilescountGenomescountProjectscountRunscountSamplescreateAppResultscreateProjectDateCreatedDisplayedCountfileCollectionfileItemFilesgenomeCollectiongenomeItemGenomesgetBAMsgetCoveragegetCoverageStatsgetFilesgetIndexedBamgetVariantsgetVariantSethasAccessHrefHrefBaseSpaceUIIdinitializeAuthItemsLimitlistAppResultslistAppSessionslistFileslistGenomeslistProjectslistRunslistSamplesNameOffsetperformOAuthprojectCollectionprojectItemProjectsputFilesrequestAccessTokenResponseStatusrunCollectionrunItemRunssampleCollectionsampleItemSamplesServiceURIshowSortBySortDirStatusTotalCountupdateAppSessionsuriuserItemUserOwnedByUsers
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 |
