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Releases: waldronlab/cBioPortalData

GitHub Release 1.0.1

07 Jan 20:05
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CHANGES IN VERSION 1.0.1

New features

  • Package supports nearly all study identifiers based on recent tests
  • Only a handful of study identifiers are unsuccessful (create an issue to
    prioritize).

Bug fixes and minor improvements

  • Make better use of the API return values to craft the sample map for
    MultiAssayExperiment creation
  • Additional data included in the metadata slot of the MultiAssayExperiment
    object. Future revisions will include this data as rowData.
  • Change vignette titles for build

CHANGES IN VERSION 0.1.0

New features

  • cBioDataPack allows users to download packaged data objects from
    download.cbioportal.org/
  • Data packs are cached using BiocFileCache to avoid re-downloading
  • cBioPortalData lets users query the cbioportal.org API and retrieve slices
    of data according to gene, molecular profile identifiers, etc.
  • Queries through cBioPortalData use a caching mechanism to avoid repeat
    downloads of data and improve load times
  • Both functions return a MultiAssayExperiment as the primary data
    representation
  • Only a number of study datasets are currently possible to load. Issues
    can arise with mismatched or munged identifiers
  • The cBioPortal API representation is handled by the AnVIL package
    which makes use of rapiclient to provide an automatic R interface to the API

Bug fixes and minor improvements

  • Data pack downloads use an alternative method for download when a download
    fails