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opalr  

'Opal' Data Repository Client and 'DataSHIELD' Utils
View on CRAN: Click here


Download and install opalr package within the R console
Install from CRAN:
install.packages("opalr")

Install from Github:
library("remotes")
install_github("cran/opalr")

Install by package version:
library("remotes")
install_version("opalr", "3.5.2")



Attach the package and use:
library("opalr")
Maintained by
Yannick Marcon
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2019-02-18
Latest Update: 2024-09-18
Description:
Data integration Web application for biobanks by 'OBiBa'. 'Opal' is the core database application for biobanks. Participant data, once collected from any data source, must be integrated and stored in a central data repository under a uniform model. 'Opal' is such a central repository. It can import, process, validate, query, analyze, report, and export data. 'Opal' is typically used in a research center to analyze the data acquired at assessment centres. Its ultimate purpose is to achieve seamless data-sharing among biobanks. This 'Opal' client allows to interact with 'Opal' web services and to perform operations on the R server side. 'DataSHIELD' administration tools are also provided.
How to cite:
Yannick Marcon (2019). opalr: 'Opal' Data Repository Client and 'DataSHIELD' Utils. R package version 3.5.2, https://cran.r-project.org/web/packages/opalr. Accessed 06 Aug. 2026.
Previous versions and publish date:
(2026-07-09 06:37), 1.0.0 (2019-02-18 11:00), 1.0.1 (2019-02-26 18:50), 1.0.2 (2019-03-19 11:40), 1.0.3 (2019-03-21 12:10), 1.1.0 (2019-06-26 13:40), 1.2.0 (2019-08-19 13:40), 1.3.0 (2019-12-10 22:10), 1.4.0 (2020-05-18 14:10), 1.4.1 (2020-06-08 11:30), 1.5.0 (2020-11-03 11:20), 1.5.1 (2020-12-16 21:00), 1.5.2 (2021-01-21 12:40), 2.0.0 (2021-03-09 13:20), 2.1.0 (2021-04-29 18:20), 2.1.1 (2021-05-31 11:20), 3.0.0 (2021-07-05 12:50), 3.0.1 (2021-08-23 13:50), 3.0.2 (2021-10-26 11:10), 3.1.0 (2022-05-02 15:00), 3.1.1 (2022-06-09 09:40), 3.2.0 (2022-10-13 11:00), 3.3.0 (2023-02-03 10:40), 3.3.1 (2023-02-28 12:12), 3.4.0 (2023-10-06 16:20), 3.4.1 (2024-01-10 20:43), 3.4.2 (2024-09-18 09:20), 3.5.0 (2025-11-05 17:40), 3.5.1 (2025-11-16 17:00), 3.5.2 (2025-12-09 17:30), 3.6.0 (2026-04-17 07:10)
Other packages that cited opalr R package
View opalr citation profile
Other R packages that opalr depends, imports, suggests or enhances
Complete documentation for opalr
Functions, R codes and Examples using the opalr R package
Some associated functions: dictionary.annotate.harmo_status . dictionary.annotate . dictionary.annotations . dictionary.apply . dictionary.inspect . dot-aclsToDataFrame . dot-as.zeroOne . dot-authorizationHeader . dot-deparse . dot-extractJsonField . dot-extractLabel . dot-extractOpalSessionId . dot-getContent . dot-getPEMFilePath . dot-getRSessionId . dot-getSessions . dot-handleError . dot-handleResponse . dot-handleResponseLocation . dot-handleResponseOrCallback . dot-is.verbose . dot-isContentEmpty . dot-listToJson . dot-newProgress . dot-newSession . dot-opal.login . dot-rmOpalSession . dot-rmRSession . dot-select . dot-tickProgress . dot-tokenHeader . dot-url . dot-verbose . dsadmin.activity . dsadmin.activity_summary . dsadmin.get_method . dsadmin.get_methods . dsadmin.get_options . dsadmin.install_github_package . dsadmin.install_local_package . dsadmin.install_package . dsadmin.installed_package . dsadmin.log . dsadmin.package_description . dsadmin.package_descriptions . dsadmin.perm . dsadmin.perm_add . dsadmin.perm_delete . dsadmin.profile . dsadmin.profile_access . dsadmin.profile_create . dsadmin.profile_delete . dsadmin.profile_enable . dsadmin.profile_exists . dsadmin.profile_init . dsadmin.profile_perm . dsadmin.profile_perm_add . dsadmin.profile_perm_delete . dsadmin.profile_rparser . dsadmin.profiles . dsadmin.publish_package . dsadmin.remove_package . dsadmin.rm_method . dsadmin.rm_methods . dsadmin.rm_option . dsadmin.rm_options . dsadmin.rm_package_methods . dsadmin.set_method . dsadmin.set_option . dsadmin.set_package_methods . dsadmin.unpublish_package . oadmin.activity . oadmin.activity_summary . oadmin.install_bioconductor_package . oadmin.install_cran_package . oadmin.install_devtools . oadmin.install_github_package . oadmin.install_local_package . oadmin.install_package . oadmin.installed_devtools . oadmin.installed_package . oadmin.installed_packages . oadmin.log . oadmin.log_rest . oadmin.log_sql . oadmin.package_description . oadmin.perm . oadmin.perm_add . oadmin.perm_delete . oadmin.r_perm . oadmin.r_perm_add . oadmin.r_perm_delete . oadmin.remove_package . oadmin.system_metrics . oadmin.system_perm . oadmin.system_perm_add . oadmin.system_perm_delete . oadmin.user_add . oadmin.user_delete . oadmin.user_enable . oadmin.user_exists . oadmin.user_profile_delete . oadmin.user_profiles . oadmin.user_reset_password . oadmin.users . opal.annotate . opal.annotations . opal.as_md_table . opal.assign.data . opal.assign . opal.assign.resource . opal.assign.script . opal.assign.table . opal.assign.table.tibble . opal.attribute_values . opal.command . opal.command_result . opal.command_rm . opal.commands . opal.commands_rm . opal.datasource . opal.datasources . opal.delete . opal.execute . opal.execute.source . opal.file . opal.file_cp . opal.file_download . opal.file_ls . opal.file_mkdir . opal.file_mkdir_tmp . opal.file_mv . opal.file_read . opal.file_rm . opal.file_unzip . opal.file_upload . opal.file_write . opal.get . opal.load_package . opal.login . opal.logout . opal.perms . opal.post . opal.profiles . opal.project . opal.project_backup . opal.project_command . opal.project_create . opal.project_delete . opal.project_exists . opal.project_perm . opal.project_perm_add . opal.project_perm_delete . opal.project_restore . opal.projects . opal.projects_databases . opal.put . opal.report . opal.report_md . opal.resource . opal.resource_create . opal.resource_delete . opal.resource_exists . opal.resource_extension_create . opal.resource_get . opal.resource_perm . opal.resource_perm_add . opal.resource_perm_delete . opal.resource_view_create . opal.resource_view_reconnect . opal.resources . opal.resources_perm . opal.resources_perm_add . opal.resources_perm_delete . opal.rm . opal.sql . opal.sql_history . opal.symbol_import . opal.symbol_rm . opal.symbol_save . opal.symbols . opal.table . opal.table_create . opal.table_delete . opal.table_dictionary_get . opal.table_dictionary_update . opal.table_exists . opal.table_export . opal.table_get . opal.table_import . opal.table_perm . opal.table_perm_add . opal.table_perm_delete . opal.table_save . opal.table_truncate . opal.table_view_create . opal.table_view_update . opal.tables . opal.tables_perm . opal.tables_perm_add . opal.tables_perm_delete . opal.task . opal.task_cancel . opal.task_wait . opal.tasks . opal.taxonomies . opal.taxonomy . opal.taxonomy_delete . opal.taxonomy_download . opal.taxonomy_upload . opal.terms . opal.token . opal.token_datashield_create . opal.token_delete . opal.token_r_create . opal.token_renew . opal.token_sql_create . opal.tokens . opal.unload_package . opal.valueset . opal.variable . opal.variable_summary . opal.variables . opal.version_compare . opal.vocabularies . opal.vocabulary . opal.workspace_restore . opal.workspace_rm . opal.workspace_save . opal.workspaces . opalr-package . 
Some associated R codes: datashield.admin.R . dictionary.R . dictionary.annotations.R . opal.R . opal.admin.R . opal.annotations.R . opal.assign.R . opal.command.R . opal.datasource.R . opal.execute.R . opal.file.R . opal.perm.R . opal.project.R . opal.report.R . opal.resource.R . opal.sql.R . opal.symbol.R . opal.table.R . opal.task.R . opal.taxonomy.R . opal.token.R . opal.users.R . opal.workspace.R . opalr-package.R . utils.R .  Full opalr package functions and examples
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