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✨
DESCRIPTION |NEWS
card.svg |card.png
Rega/json (API)

# 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-1.1.1(bioc 3.24)Rega-1.0.2(bioc 3.23)

software infrastructure thirdpartyclient

5.02 score 3 scripts 203 downloads 65 exports 42 dependencies

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

Target	Result	Time
bioc-checks	NOTE	162
linux-devel-x86_64	OK	315
source / vignettes	OK	216
linux-release-x86_64	OK	355
macos-release-arm64	OK	141
macos-oldrel-arm64	OK	131
windows-devel	OK	117
windows-release	OK	117
windows-oldrel	OK	115
wasm-release	OK	127

Exports:add_required_str aliases_formatter api_function_factory api_name_to_label column_table_formatter create_client default_parser default_validator delete_submission delete_submission_contents DELIM_CONVERTERS ega_oauth ega_token extract_api extract_operation_definitions extract_resource_name fetch_files file_formatter filter_id_fields finalise_submission first_row_to_colnames fold_column format_chromosomes get_chr_group get_entry_by_title get_enum get_formatter get_formatter_params get_operation_schema get_or_post get_properties get_schemas get_sentence_number get_submission get_word_number has_linked_sheets is_accession is_provisional is_valid_http_method label_to_api_name link_sheet lut_add merge_linked_sheet multi_lut_add na_to_empty_list new_submission parse_ega_body parse_enum parse_json_body parse_text_body process_chromosomes process_delimited_column rollback_submission row_table_formatter samples_in_db save_log step_msg submit_table try_step unbox_list unbox_row use_submission validate_schema validation_to_msg workflow_error_handler

Dependencies:askpass cellranger cli cpp11 crayon curl dplyr filelock generics glue hms httr2 jsonlite jsonvalidate keyring lifecycle magrittr openssl pillar pkgconfig prettyunits progress purrr R6 rappdirs Rcpp readxl rematch rlang settings stringi stringr sys tibble tidyr tidyselect utf8 V8 validate vctrs withr yaml

The Rega User Guide

Rendered fromRega.Rmdusingknitr::rmarkdown

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Mark Required Fields with a Prefix	add_required_str
Format Aliases from a Table	aliases_formatter
Generate an API Function from Operation and Specification	api_function_factory
Convert API Names to Prettified Labels	api_name_to_label
Format a Column Table	column_table_formatter
Generate API Client Functions	create_client
Parser for a Default EGA Excel Template	default_parser
Validator for Default Parser	default_validator
Delete a Submission and Log Responses	delete_submission
Delete Submission Contents and Log Responses	delete_submission_contents
Default Column Converters for EGA Metadata	DELIM_CONVERTERS
Set The OAUTH With EGA Username And Password	ega_oauth
Retrieve EGA API Bearer Token	ega_token
Extract API Specification and Host Details	extract_api
Extract API Operation Definitions	extract_operation_definitions
Extract Resource Name from API Response URL	extract_resource_name
Fetch file information from EGA inbox	fetch_files
Format File Table with EGA File Paths	file_formatter
Filter Out ID Fields from a Character Vector	filter_id_fields
Finalise an EGA submission	finalise_submission
Use First Row as Column Names for a Data Frame	first_row_to_colnames
Fold Columns with a Common Prefix into a Single Column Nested as List	fold_column
Format Chromosome Metadata	format_chromosomes
Retrieve Chromosome Belonging to a Group	get_chr_group
Retrieve EGA entries by title	get_entry_by_title
Retrieve Enum Values from an API	get_enum
Retrieve a Formatter Function by Type of Submission Metadata Table	get_formatter
Retrieve Formatter Parameters by Name	get_formatter_params
Retrieve the Schema for an API Operation	get_operation_schema
Retrieve or Submit Data to an EGA API Endpoint	get_or_post
Extract and Format Properties from a Schema	get_properties
Retrieve Request schemas from an API Specification	get_schemas
Count the number of sentences in text	get_sentence_number
Retrieve Submission Data and Log Responses	get_submission
Count the number of words in text	get_word_number
Check for Linked Sheets in Metadata	has_linked_sheets
Check if a String is a Valid Accession Identifier.	is_accession
Check whether IDs is a provisional ID.	is_provisional
Validate HTTP Method	is_valid_http_method
Convert Prettified Labels to API Names	label_to_api_name
Link Data Between Metadata Sheets	link_sheet
Add a Column to a Data Frame Based on Lookup Table	lut_add
Merge Linked Sheets with Source Data	merge_linked_sheet
Add Multiple Lookup-Based Columns to a Data Frame	multi_lut_add
Convert NA Values to Empty Lists	na_to_empty_list
Submit New Data to EGA	new_submission
Parse The Information From EGA httr2 Response Object.	parse_ega_body
Parse Enum into a Formatted String	parse_enum
Parse and Standardize JSON Response Body	parse_json_body
Parse Plain Text or JSON-like Response Body	parse_text_body
Process a Vector or List of Chromosome Data	process_chromosomes
Process Delimited Columns in Metadata	process_delimited_column
Rollback Submission Endpoints and Log Responses	rollback_submission
Format a Row Table	row_table_formatter
Check if sample aliases exist in the EGA database	samples_in_db
Save API Responses to a Log File	save_log
Generate a Step-by-Step Message Function	step_msg
Submit a Data Frame to an API Endpoint Row by Row	submit_table
Execute a submission step with error handling and rollback	try_step
Convert a List to an Unboxed JSON-Compatible Data Frame	unbox_list
Convert a Data Frame Row to an Unboxed JSON Object	unbox_row
Retrieve or Delete Submission Data	use_submission
Validate a Payload Against a JSON Schema	validate_schema
Convert Validation Results to a Message	validation_to_msg
Workflow Error Handler	workflow_error_handler