NEWS

Changes in version 0.0.1 (2019-02-01)
+ Added direct support for `seurat` and other object classes
+ Updated readme and tutorial pages
+ Moved some larger reference data to `clustifyrdata`

Changes in version 0.0.2 (2019-05-29)
+ Updated discussions, benchmark, and visualization example pages
+ Reorganized `clustifyrdata` data package

Changes in version 0.0.3 (2019-09-06)
+ Support of SingleCellExperiment objects and more
+ Bug fixes

Changes in version 0.99.0 (2019-11-06)
+ Update to tutorials
+ Refactor arguments
+ Bug fixes
+ Cleanup for Bioconductor submission

Changes in version 1.1.0 (2020-05-21)
+ Bioc release
+ Bug fixes

Changes in version 1.1.2 (2020-09-21)
+ USCS cell browser reference building
+ Tutorial update
+ Bug fixes

Changes in version 1.3.1 (2020-12-26)
+ Q&A section
+ Now defaults to top 1000 variable genes in Seurat (including v4)
+ Bug fixes

Changes in version 1.3.2 (2021-02-25)
+ `build_atlas()` for combining references
+ More Q&A

Changes in version 1.3.3 (2021-02-28)
+ Launch shiny app with `run_clustifyr_app()`
+ Plot and GO for most divergent ranks in correlation of query vs reference

Changes in version 1.5.1 (2021-08-04)
+ `clustify_lists()` support for uneven number of markers
+ Deprecated SeuratV2 support

Changes in version 1.5.2 (2021-10-04)
+ `clustify_lists()` support for output of overlapping genes (`details_out = TRUE`)
+ Added truncated mean and trimean modes to `average_clusters()`

Changes in version 1.7.3 (2022-03-09)
+ `vec_out` option for directly getting classification results as a vector, to be inserted into other metadata/workflow
+ Maintainer change

Changes in version 1.15.1 (2023-10-31)
+ Replace `Seurat` dependency with `SeuratObject`

Changes in version 1.15.2 (2024-04-03)
+ Add support for `Seurat` version 5 objects