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Changelog

Source: NEWS.md

tiledbsoma 1.6.0

Fixes

  • SOMADataFrame, SOMASparseNDArray, and SOMADenseNDArray’s write() method now correctly leaves the array open in write mode

tiledbsoma 1.5.0

Changes

  • Add support for I/O of R factors as enumerated types in SOMADataFrame
  • Add support for writing SummarizedExperiment and SingleCellExperiment object to SOMAs
  • Add support for bounding boxes for sparse arrays
  • Add support for creating SOMADataFrames with ordered() columns
  • Add support for I/O between SOMA and SingleCellExperiment
  • Add support for updating obs and var
  • Write string attrs as UTF-8 (Python compatibility)
  • Optimize export of obsm/varm arrays to Seurat
  • Add axis_query() method to SOMAExperiment
  • Add to_sparse_matrix() method to SOMAExperimentAxisQuery
  • Force exporting v3 assays with SeuratObject v5 installed

tiledbsoma 1.4.0

This is the initial release of the tiledbsoma R package.

Changes

  • Added a NEWS.md file to track changes to the package
  • TileDBGroup gains a names method to retrieve the names of group members
  • Added SOMAMeasurement and SOMAExperiment classes
  • spdl is now used for logging
  • TileDB performance statistics can now be collected for analysis
  • Added support for performing axis-based queries against a SOMAExperiment via the SOMAExperimentAxisQuery class
  • TileDBArray class gained a colnames() method that returns the names of both dimensions and attributes
  • Added internal helpers to centrally validate coords and value_filter arguments
  • All R6 classes’ create() method now return self rather than nothing
  • Fixed calculating of relative paths when 1 of the URIs contains the file:// prefix
  • Added PlatformConfig and SOMATileDBContext classes to handle SOMA and TileDB configuration
  • Add Seurat outgestors for SOMAExperimentAxisQuery objects
  • Numeric coordinates passed to SOMADataFrame$read() are now automatically upcast to int64 when necessary
  • Add ingestors to read data from Seurat objects
  • Add methods for listing and accessing bundled datasets, which now includes a SOMAExperiment containing the pbmc_small dataset from the SeuratObject package
  • New vignettes describing SOMA objects, reading data from them, and querying SOMA experiments
  • Objects added to SOMACollection-based classes using the add_new_*() methods now pass through their parent context and platform config
  • SOMAExperimentAxisQuery gained a to_sparse_matrix() method for retrieving data as a named sparse matrix
  • SOMAExperiment gained axis_query() to construct a SOMAExperimentAxisQuery object
  • Add SingleCellExperiment outgestor for SOMAExperimentAxisQuery objects