Changes

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

Added

  • Add keys to Assays and DimReducs in UpdateSeuratObject when missing

Changed

  • Bump required Matrix version to >= 1.5.0

Changed

  • Update sparse matrix coersions due to Matrix deprecations

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

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

Changed

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

Changed

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

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)
  • Initial release of SeuratObject