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biocompute

Seven Bridges implementation of the BioCompute Object (BCO) specification. Offers the capabilities to compose, validate, and convert BioCompute Objects with R.

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.

Check out the introduction vignette or the case study vignette to get started.

Installation

To download and install biocompute from CRAN:

install.packages("biocompute")

Or try the development version on GitHub:

# install.packages("remotes")
remotes::install_github("sbg/biocompute")

Copyright

© 2021 Seven Bridges Genomics, Inc. All rights reserved.

This project is licensed under the GNU Affero General Public License v3.

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Version

Install

install.packages('biocompute')

Monthly Downloads

204

Version

1.1.1

License

AGPL-3

Issues

1

Pull Requests

0

Stars

3

Forks

3

Maintainer

Soner Koc

Last Published

May 3rd, 2022

Functions in biocompute (1.1.1)

compose_usability_v1.4.2

Compose BioCompute Object - Usability Domain (v1.4.2)
versions

BioCompute Object specification versions
export_pdf

Export BioCompute Object as PDF
read_bco

Parse Biocompute Object From JSON File to R Object
export_json

Export BioCompute Object as JSON
%>%

Pipe operator
convert_json

Convert BioCompute Object or domain to JSON string
generate_id

Generate ID for the BioCompute Object
export_html

Export BioCompute Object as HTML
generate_example

Generate example BioCompute Objects
convert_yaml

Convert BioCompute Object or domain to YAML string
export_sevenbridges

Export BioCompute Object to Seven Bridges Platforms
is_bco

Is this a BCO object?
export_word

Export BioCompute Object as Word document
is_domain

Is this a domain object?
compose_scm_v1.4.2

Compose BioCompute Object - SCM Extension (v1.4.2)
compose_extension_v1.4.2

Compose BioCompute Object - Extension Domain (v1.4.2)
compose_tlf_v1.4.2

Compose BioCompute Object - Top Level Fields (v1.4.2)
validate_schema_v1.4.2

BioCompute Objects schema validator (v1.4.2)
validate_checksum_v1.4.2

BioCompute Objects checksum validator (v1.4.2)
compose_provenance_v1.4.2

Compose BioCompute Object - Provenance Domain (v1.4.2)
compose_error_v1.4.2

Compose BioCompute Object - Error Domain (v1.4.2)
compose_execution_v1.4.2

Compose BioCompute Object - Execution Domain (v1.4.2)
compose_fhir_v1.4.2

Compose BioCompute Object - FHIR Extension (v1.4.2)
compose_description_v1.4.2

Compose BioCompute Object - Description Domain (v1.4.2)
compose_parametric_v1.4.2

Compose BioCompute Object - Parametric Domain (v1.4.2)
compose_v1.4.2

Compose BioCompute Object (v1.4.2)
biocompute-package

biocompute: Create and Manipulate BioCompute Objects
compose_io_v1.4.2

Compose BioCompute Object - Input and Output Domain (v1.4.2)