Package: Rega 1.1.1

Igor Cervenka

Rega: R Interface to European Genome-Phenome Archive

The European Genome-phenome Archive (EGA) provides long-term storage and controlled sharing of personally identifiable genetic data. The Rega package offers a streamlined and extensible R interface to the EGA API, facilitating the programmatic upload of metadata. GEO-like Excel submission template is provided as a default method of organizing submission metadata.

Authors:Igor Cervenka [aut, cre], Athimed El Taher [aut], Robert Ivanek [aut]

Rega_1.1.1.tar.gz
Rega_1.1.1.zip(r-4.7)Rega_1.1.1.zip(r-4.6)Rega_1.1.1.zip(r-4.5)
Rega_1.1.1.tgz(r-4.6-any)Rega_1.1.1.tgz(r-4.5-any)
Rega_1.1.1.tar.gz(r-4.7-any)Rega_1.1.1.tar.gz(r-4.6-any)
Rega_1.1.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
Rega/json (API)
NEWS

# Install 'Rega' in R:
install.packages('Rega', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/ivanek/rega/issues

On BioConductor:Rega-1.1.0(bioc 3.24)Rega-1.0.0(bioc 3.23)

softwareinfrastructurethirdpartyclient

5.02 score 3 scripts 132 downloads 65 exports 42 dependencies

Last updated from:5023676d93. Checks:1 NOTE, 9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE153
linux-devel-x86_64OK182
source / vignettesOK179
linux-release-x86_64OK210
macos-release-arm64OK108
macos-oldrel-arm64OK132
windows-develOK132
windows-releaseOK117
windows-oldrelOK127
wasm-releaseOK118

Exports:add_required_straliases_formatterapi_function_factoryapi_name_to_labelcolumn_table_formattercreate_clientdefault_parserdefault_validatordelete_submissiondelete_submission_contentsDELIM_CONVERTERSega_oauthega_tokenextract_apiextract_operation_definitionsextract_resource_namefetch_filesfile_formatterfilter_id_fieldsfinalise_submissionfirst_row_to_colnamesfold_columnformat_chromosomesget_chr_groupget_entry_by_titleget_enumget_formatterget_formatter_paramsget_operation_schemaget_or_postget_propertiesget_schemasget_sentence_numberget_submissionget_word_numberhas_linked_sheetsis_accessionis_provisionalis_valid_http_methodlabel_to_api_namelink_sheetlut_addmerge_linked_sheetmulti_lut_addna_to_empty_listnew_submissionparse_ega_bodyparse_enumparse_json_bodyparse_text_bodyprocess_chromosomesprocess_delimited_columnrollback_submissionrow_table_formattersamples_in_dbsave_logstep_msgsubmit_tabletry_stepunbox_listunbox_rowuse_submissionvalidate_schemavalidation_to_msgworkflow_error_handler

Dependencies:askpasscellrangerclicpp11crayoncurldplyrfilelockgenericsgluehmshttr2jsonlitejsonvalidatekeyringlifecyclemagrittropensslpillarpkgconfigprettyunitsprogresspurrrR6rappdirsRcppreadxlrematchrlangsettingsstringistringrsystibbletidyrtidyselectutf8V8validatevctrswithryaml

The Rega User Guide

Igor Cervenka, Athimed El Taher, Robert Ivánek

Rendered fromRega.Rmdusingknitr::rmarkdownon Jun 09 2026.

Last update: 2026-02-02
Started: 2023-04-21

Readme and manuals

Help Manual

Help pageTopics
Mark Required Fields with a Prefixadd_required_str
Format Aliases from a Tablealiases_formatter
Generate an API Function from Operation and Specificationapi_function_factory
Convert API Names to Prettified Labelsapi_name_to_label
Format a Column Tablecolumn_table_formatter
Generate API Client Functionscreate_client
Parser for a Default EGA Excel Templatedefault_parser
Validator for Default Parserdefault_validator
Delete a Submission and Log Responsesdelete_submission
Delete Submission Contents and Log Responsesdelete_submission_contents
Default Column Converters for EGA MetadataDELIM_CONVERTERS
Set The OAUTH With EGA Username And Passwordega_oauth
Retrieve EGA API Bearer Tokenega_token
Extract API Specification and Host Detailsextract_api
Extract API Operation Definitionsextract_operation_definitions
Extract Resource Name from API Response URLextract_resource_name
Fetch file information from EGA inboxfetch_files
Format File Table with EGA File Pathsfile_formatter
Filter Out ID Fields from a Character Vectorfilter_id_fields
Finalise an EGA submissionfinalise_submission
Use First Row as Column Names for a Data Framefirst_row_to_colnames
Fold Columns with a Common Prefix into a Single Column Nested as Listfold_column
Format Chromosome Metadataformat_chromosomes
Retrieve Chromosome Belonging to a Groupget_chr_group
Retrieve EGA entries by titleget_entry_by_title
Retrieve Enum Values from an APIget_enum
Retrieve a Formatter Function by Type of Submission Metadata Tableget_formatter
Retrieve Formatter Parameters by Nameget_formatter_params
Retrieve the Schema for an API Operationget_operation_schema
Retrieve or Submit Data to an EGA API Endpointget_or_post
Extract and Format Properties from a Schemaget_properties
Retrieve Request schemas from an API Specificationget_schemas
Count the number of sentences in textget_sentence_number
Retrieve Submission Data and Log Responsesget_submission
Count the number of words in textget_word_number
Check for Linked Sheets in Metadatahas_linked_sheets
Check if a String is a Valid Accession Identifier.is_accession
Check whether IDs is a provisional ID.is_provisional
Validate HTTP Methodis_valid_http_method
Convert Prettified Labels to API Nameslabel_to_api_name
Link Data Between Metadata Sheetslink_sheet
Add a Column to a Data Frame Based on Lookup Tablelut_add
Merge Linked Sheets with Source Datamerge_linked_sheet
Add Multiple Lookup-Based Columns to a Data Framemulti_lut_add
Convert NA Values to Empty Listsna_to_empty_list
Submit New Data to EGAnew_submission
Parse The Information From EGA httr2 Response Object.parse_ega_body
Parse Enum into a Formatted Stringparse_enum
Parse and Standardize JSON Response Bodyparse_json_body
Parse Plain Text or JSON-like Response Bodyparse_text_body
Process a Vector or List of Chromosome Dataprocess_chromosomes
Process Delimited Columns in Metadataprocess_delimited_column
Rollback Submission Endpoints and Log Responsesrollback_submission
Format a Row Tablerow_table_formatter
Check if sample aliases exist in the EGA databasesamples_in_db
Save API Responses to a Log Filesave_log
Generate a Step-by-Step Message Functionstep_msg
Submit a Data Frame to an API Endpoint Row by Rowsubmit_table
Execute a submission step with error handling and rollbacktry_step
Convert a List to an Unboxed JSON-Compatible Data Frameunbox_list
Convert a Data Frame Row to an Unboxed JSON Objectunbox_row
Retrieve or Delete Submission Datause_submission
Validate a Payload Against a JSON Schemavalidate_schema
Convert Validation Results to a Messagevalidation_to_msg
Workflow Error Handlerworkflow_error_handler