NEWS

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SeuratObject 4.1.4 (2023-09-26)

Changes

• Fixes for CellsByIdentities (#80)
• Remove {rgeos} from Suggests and replace with {sf} due to {rgeos} package retirement
• New check for potential binary breaks between dependencies and SeuratObject

SeuratObject 4.1.3 (2022-11-07)

Changes

• Move {rgeos} to Suggests; segmentation simplification now requires {rgeos} to be installed manually
• Move {sp} to Depends

Added

• Add keys to Assays and DimReducs in UpdateSeuratObject when missing

SeuratObject 4.1.2 (2022-09-20)

Changed

• Bump required Matrix version to >= 1.5.0

SeuratObject 4.1.1 (2022-08-29)

Changed

• Update sparse matrix coersions due to Matrix deprecations

SeuratObject 4.1.0 (2022-05-01)

Changed

• Allow UpdateSeuratObject to work when data is NULL (#38)
• Fix superclass issue with R-devel 4.3.x (#42)

Added

• New FOV, Segmentations, Centroids, and Molecules classes for imaging-based spatial datasets

SeuratObject 4.0.4 (2021-11-23)

Changed

• CreateSeuratObject.Assay sets Assay key when not present (#29)
• Ignore warnings when creating an Assay from a data frame (#32)

Added

• New CheckMatrix generic for validating expression matrices

SeuratObject 4.0.3 (2021-11-10)

Changed

• Export utility functions (#22)
• Bug fix in names with Key.Seurat (#26)
• Improved duplicate key checking and resolution

SeuratObject 4.0.2 (2021-06-09)

Changed

• Provide default option for Seurat.checkdots option if option is not set (#16)

SeuratObject 4.0.1 (2021-05-08)

Added

• head and tail methods for Seurat and Assay objects (#5)
• New utility functions (#6):
  • AttachDeps to attach required imported dependencies on package attachment
  • IsMatrixEmpty to test if a matrix is empty or not

Changed

• Allow super classes to replace child classes (#1). For example, allows Assay objects to replace Seurat::SCTAssay or Signac::ChromatinAssay objects of the same name
• Better support for creating sparse matrices from data.table/tibble objects (#4)
• Improved error messages for clashing object names (#7)
• Allow returning a NULL if a subset results in zero cells (#9)

Removed

• SCT-specific code (#2)

SeuratObject 4.0.0 (2021-01-15)

• Initial release of SeuratObject