Changes in version 2.8.0                        

New features

  - Auth token string or file can now be included in the cBioPortal
    function.
  - The check_build argument can be set to FALSE for alternative APIs,
    e.g., KidsFirst, when using cBioPortalData
  - queryGeneTable translates gene IDs ('hugoGeneSymbols' <>
    'entrezGeneIds') via the API service
  - getDataByGenes supersedes getDataByGenePanel
  - getStudies() replaces data('studiesTable') to discover study IDs

Bug fixes and minor improvements

  - Fixed issue where the by argument was not passed to getDataByGenes
    in internal calls
  - Add names to metadata elements that originate from GISTIC datasets.

                        Changes in version 2.6.0                        

New features

  - A study's build status can be obtained from getStudies(), which has
    replaced data('studiesTable').
  - Partial loading of data files supported. A warning is emitted when a
    data file is not able to be loaded in cBioDataPack.
  - cBioPortalData checks the data(studiesTable) to verify that study
    datasets are building, otherwise provide a message in interactive
    sessions.

                        Changes in version 2.4.0                        

New features

  - Vignettes include additional information (#38, @lwaldron)
  - getDataByGenePanel deprecated for getDataByGenes which handles input
    of both gene panels and genes
  - cBioPortalData now allows for gene inputs as either Entrez IDs or
    Hugo symbols (#24, @jucor) and sampleIds input
  - When gene inputs are provided, the by argument has to agree with the
    type of genes provided (either be entrezGeneId or hugoGeneSymbol).

Bug fixes and minor improvements

  - Fixed an issue where the labels in the metadata from cBioDataPack
    were missing ('LICENSE' and 'Fusion'; #37)
  - loadStudy allows cleanup=TRUE for removing files after untar-ing
  - Published article now available with citation("cBioPortalData")

                        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