Package: biocompute 1.1.1

Soner Koc

biocompute: Create and Manipulate BioCompute Objects

Tools to create, validate, and export BioCompute Objects described in King et al. (2019) <doi:10.17605/osf.io/h59uh>. Users can encode information in data frames, and compose BioCompute Objects from the domains defined by the standard. A checksum validator and a JSON schema validator are provided. This package also supports exporting BioCompute Objects as JSON, PDF, HTML, or 'Word' documents, and exporting to cloud-based platforms.

Authors:Soner Koc [aut, cre], Jeffrey Grover [aut], Nan Xiao [aut], Dennis Dean [aut], Seven Bridges Genomics [cph, fnd]

biocompute_1.1.1.tar.gz
biocompute_1.1.1.zip(r-4.5)biocompute_1.1.1.zip(r-4.4)biocompute_1.1.1.zip(r-4.3)
biocompute_1.1.1.tgz(r-4.4-any)biocompute_1.1.1.tgz(r-4.3-any)
biocompute_1.1.1.tar.gz(r-4.5-noble)biocompute_1.1.1.tar.gz(r-4.4-noble)
biocompute_1.1.1.tgz(r-4.4-emscripten)biocompute_1.1.1.tgz(r-4.3-emscripten)
biocompute.pdf |biocompute.html✨
biocompute/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/sbg/biocompute/issues

On CRAN:

biocomputebiocompute-objectsbioinformaticsscience-communicationsevenbridgesstandardizationworkflow

4.07 score 3 stars 13 scripts 252 downloads 1 mentions 42 exports 40 dependencies

Last updated 6 months agofrom:a7afdada6a. Checks:ERROR: 7. Indexed: yes.

TargetResultDate
Doc / VignettesFAILNov 06 2024
R-4.5-winERRORNov 06 2024
R-4.5-linuxERRORNov 06 2024
R-4.4-winERRORNov 06 2024
R-4.4-macERRORNov 06 2024
R-4.3-winERRORNov 06 2024
R-4.3-macERRORNov 06 2024

Exports:%>%composecompose_descriptioncompose_description_v1.4.2compose_errorcompose_error_v1.4.2compose_executioncompose_execution_v1.4.2compose_extensioncompose_extension_v1.4.2compose_fhircompose_fhir_v1.4.2compose_iocompose_io_v1.4.2compose_parametriccompose_parametric_v1.4.2compose_provenancecompose_provenance_v1.4.2compose_scmcompose_scm_v1.4.2compose_tlfcompose_tlf_v1.4.2compose_usabilitycompose_usability_v1.4.2compose_v1.4.2convert_jsonconvert_yamlexport_htmlexport_jsonexport_pdfexport_sevenbridgesexport_wordgenerate_examplegenerate_idis_bcois_domainread_bcovalidate_checksumvalidate_checksum_v1.4.2validate_schemavalidate_schema_v1.4.2versions

Dependencies:askpassbase64encbslibcachemclicrayoncurldigestevaluatefastmapfontawesomefsgluehighrhtmltoolshttrjquerylibjsonlitejsonvalidateknitrlifecyclemagrittrmemoisemimeopensslR6rappdirsRcpprlangrmarkdownsassstringistringrsystinytexuuidV8vctrsxfunyaml

Readme and manuals

Help Manual

Help pageTopics
Compose BioCompute Object - Description Domain (v1.4.2)compose_description compose_description_v1.4.2
Compose BioCompute Object - Error Domain (v1.4.2)compose_error compose_error_v1.4.2
Compose BioCompute Object - Execution Domain (v1.4.2)compose_execution compose_execution_v1.4.2
Compose BioCompute Object - Extension Domain (v1.4.2)compose_extension compose_extension_v1.4.2
Compose BioCompute Object - FHIR Extension (v1.4.2)compose_fhir compose_fhir_v1.4.2
Compose BioCompute Object - Input and Output Domain (v1.4.2)compose_io compose_io_v1.4.2
Compose BioCompute Object - Parametric Domain (v1.4.2)compose_parametric compose_parametric_v1.4.2
Compose BioCompute Object - Provenance Domain (v1.4.2)compose_provenance compose_provenance_v1.4.2
Compose BioCompute Object - SCM Extension (v1.4.2)compose_scm compose_scm_v1.4.2
Compose BioCompute Object - Top Level Fields (v1.4.2)compose_tlf compose_tlf_v1.4.2
Compose BioCompute Object - Usability Domain (v1.4.2)compose_usability compose_usability_v1.4.2
Compose BioCompute Object (v1.4.2)compose compose_v1.4.2
Convert BioCompute Object or domain to JSON stringconvert_json
Convert BioCompute Object or domain to YAML stringconvert_yaml
Export BioCompute Object as HTMLexport_html
Export BioCompute Object as JSONexport_json
Export BioCompute Object as PDFexport_pdf
Export BioCompute Object to Seven Bridges Platformsexport_sevenbridges
Export BioCompute Object as Word documentexport_word
Generate example BioCompute Objectsgenerate_example
Generate ID for the BioCompute Objectgenerate_id
Is this a BCO object?is_bco
Is this a domain object?is_domain
Parse Biocompute Object From JSON File to R Objectread_bco
BioCompute Objects checksum validator (v1.4.2)validate_checksum validate_checksum_v1.4.2
BioCompute Objects schema validator (v1.4.2)validate_schema validate_schema_v1.4.2
BioCompute Object specification versionsversions