Changes in version 0.5.0 (2023-11-04)                  

Changes

  - Azimuth ATAC
      - Functionality added to RunAzimuth() (vignette here), to
        AzimuthApp, and to the Azimuth Website to support sc/snATAC-seq
        queries.
  - Compatibility with Seurat v5

                 Changes in version 0.4.6 (2022-08-23)                  

Changes

  - Compatibility fix for uwot >=v0.1.13 due to changes in UMAP model
    parameters

                 Changes in version 0.4.5 (2022-04-27)                  

Changes

  - RunAzimuth() added to support local annotation.
  - LoadH5AD() assumes matrix is CSR if metadata to resolve matrix type
    is unavailable.
  - Bug fix for anndata files containing cells with 0 counts.
  - Options to set default filtering thresholds (e.g.
    Azimuth.app.ncount_max)

                 Changes in version 0.4.4 (2022-03-08)                  

Changes

  - LoadH5AD() now supports H5AD files containing CSC matrices at X or
    X/raw. Previously only CSR matrices were readable.

                 Changes in version 0.4.3 (2021-08-18)                  

Changes

  - Bug fix for cell renaming when interactively subsetting
  - Bug fix for references created with fewer than 50 dimensions

                 Changes in version 0.4.2 (2021-07-28)                  

Changes

  - Demo dataset is now optional
  - Add default hosted homolog file location
  - Bug fix when query cell name(s) overlap with reference names
  - Bug fix for Windows path specification for the reference directory

                 Changes in version 0.4.1 (2021-06-01)                  

Added

  - Ability to download all Azimuth results on Downloads tab

                 Changes in version 0.4.0 (2021-05-04)                  

Added

  - Option to have meta.data in reference that will display on hover but
    not be transferable via Azimuth.app.metadata_notransfer
  - Option to display meta.data table in heatmap form with
    Azimuth.app.metatableheatmap
  - Option to switch default DimPlot display in the cell plots tab to
    show the query overlayed on the reference with
    Azimuth.app.overlayedreference
  - Expose the dims parameter to FindTransferAnchors and TransferData as
    an option, Azimuth.map.ndims
  - ConvertGeneNames function to convert human/mouse, ensemble gene
    names. Location of conversion table file given by
    Azimuth.app.homologs.
  - Option to have multiple demo buttons. This can be configured via the
    Azimuth.app.demodatasets option.

                 Changes in version 0.3.2 (2021-03-23)                  

Added

  - LoadFileInput() and LoadReference() are now exported functions

Changes

  - Fix to prevent error when no demo dataset is provided
  - Bug fixes in template analysis script generation
  - Fix neighbor graph used for clustering in ClusterPreservationScore()

                 Changes in version 0.3.1 (2021-03-12)                  

Changes

  - Loading query datasets now filters out cells with zero counts and
    features with zero counts.