Changes in version 2.2.0                        

New features

  - studiesTable includes additional columns pack_build and api_build to
    indicate to the user which datasets have been successfully built as
    MultiAssayExperiment objects. Users will be notified when a dataset,
    reported as not building, is requested from the cBioDataPack
    function.
  - Add sampleIds argument to getDataByGenePanel as part of cache
    re-work
  - Allow more flexibility in the hostname when accessing the API with
    cBioPortal (@inodb, #16)
  - cBioDataPack downloads from a more robust repository (AWS S3;
    @inodb, #22)
  - removePackCache and removeDataCache now remove data from the user's
    cache based on inputs to respective functions (cBioDataPack and
    cBioPortalData)

Bug fixes and minor improvements

  - Attempt to merge additional clinical data files from tarballs in
    cBioDataPack.
  - Switch to using read.delim instead of read_tsv internally to avoid
    assigning NA to chromosome column
  - Use 'PATIENT_ID' when available to determine if experiment data is
    provided in the tarball files.
  - Add tests using testthat
  - Update and include percentages of studies successfully imported
    using cBioDataPack and cBioPortalData in the documentation
  - Fix read-in when identifiers are numeric instead of character
    (@jucor, #27)
  - Include pagination parameters in geneTable function (@xinwei-sher,
    #29)

                        Changes in version 2.0.0                        

New features

  - Bioconductor release!
  - Updated the README.md file from R Markdown file.
  - Uses the latest version of rapiclient on CRAN
  - Prepare package for Bioconductor submission
  - Include protein metadata as a RaggedExperiment from mutation
    molecular profiles (TCGA only)

Bug fixes and minor improvements

  - API authentication option removed and not needed

                        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