NEWS

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Azimuth 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

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.