cbioportalR - cbioportalR 1.1.1

• Fixed bug in available_studies() that arose with underlying API change from V2 to V3.
• Added lookup_id() function to return all samples that exist across cBioPortal for a given patient ID (#65).
• Re-submitted to CRAN after removed due to linux issues

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Published by karissawhiting over 1 year ago

cbioportalR - cbioportalR 1.1.0

• Added available_sample_lists() function which returns all available sample list IDs for a given study ID
• Added sample_list_id argument to available_samples() which returns all samples IDs in specific sample list within a study (#53).
• Fixed {cli} errors to make package compatible with {cli} ≥ v3.4.1.
• Added CNA segmentation retrieval endpoint accessible via get_segments_by_sample() and get_segments_by_study()). You can use get_genomics_by_*(return_segments = TRUE) as well to access this data.

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Published by karissawhiting over 2 years ago

cbioportalR - cbioportalR 1.0.1

This version makes the package compatible with cBioPortal v5.0. Main updates include:

• Fusion API endpoint URLs updated to use structural-variant instead of fusion in specification.
• get_structural_variants_by_sample() and get_structural_variants_by_study() added as aliases for get_fusions_by_sample() and get_fusions_by_study(). These functions return the same results as their fusion counterparts and both names will be supported.
• When functions include the data_type argument, structural_variant is now available as option. This will return the same results as fusion.
• Output of get_genetics_by_sample() and get_genetics_by_study() functions are now named lists with names: mutation, cna, and structural_variant (changed from fusion) to be consistent with cBioPortal v5.0 naming conventions.
• Tests and examples are no longer run on CRAN to protect from future changes to internal database. They are still run in Github Actions and examples are run on website.
• Some examples adjusted to use a new cBioPortal profile name, as needed (e.g. prad_msk_2019_structural_variants -> prad_msk_2019_structural_variants)
• bug fix in add_hugo argument of get_*_by_sample() functions.

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Published by karissawhiting over 3 years ago

cbioportalR - cbioportalR 1.0.0

This is the first release submitted to CRAN, and includes all updates made since last Github release v0.1.0 (see NEWS for details on intermediate pre-CRAN versions). Package has been overhauled since first release (v0.1.0), and code will not be backwards compatible with that version. Future versions will be backwards compatible with v1.0.0.

Summary of Updates (since 0.1.0)

• Authentication schema has been updated. Package-level environmental variable can now be set that specifies login credentials for that session
• Functionality to pull fusion data has been added
• Users can pull data by study ID, sample ID, and patient ID
• Update get_genomics_by_sample() and related functions to pull all gene data available for select samples instead of pulling data for IMPACT genes only by default
• Allow users to pass Hugo Symbols or Panel IDs to all get_genomics_by_sample() and related functions.

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Published by karissawhiting almost 4 years ago

cbioportalR - cbioportalR 0.1.0

• First release

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Published by karissawhiting over 4 years ago