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NEWS.md

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Azimuth 0.5.0 (2023-11-04)

Changes

  • Azimuth ATAC
  • Compatibility with Seurat v5

Azimuth 0.4.6 (2022-08-23)

Changes

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

Azimuth 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)

Azimuth 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.

Azimuth 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

Azimuth 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

Azimuth 0.4.1 (2021-06-01)

Added

  • Ability to download all Azimuth results on Downloads tab

Azimuth 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.

Azimuth 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()

Azimuth 0.3.1 (2021-03-12)

Changes

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