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SpatialDDLS 0.1.0 (2023-04-08)

• Added a NEWS.md file to track changes.

SpatialDDLS 0.2.0 (2023-10-04)

• Added a vignette explaining HDF5 file usage (hdf5Backend.Rmd vignette).
• Mixed transcriptional profiles are now stored as raw counts rather than normalized values in order to make calculations more transparent.
• Scale factor for normalization can be chosen (10e3 is now the default option).

SpatialDDLS 1.0.0 (2023-12-05)

• Regularization of predicted cell proportions incorporated. Functions and classes relying on the deconvSpatialDDLS function have been modified.
• Added a set of functions for clustering analysis based on predicted cell proportions (spatialClustering.R file).
• Added a module for neural network interpretation based on the vanilla gradient algorithm (interGradientsDL.R file).
• Changes in default parameters and vignette updated.

SpatialDDLS 1.0.1 (2024-02-07)

• Change in HDF5 file usage: new version of the HDF5Array package does not support “for.use” argument.
• In createSpatialDDLSobject, included the sc.log.FC parameter to optionally choose if filtering genes according to logFC.

SpatialDDLS 1.0.2 (2024-03-21)

• Included two parameters to control python and tensorflow versions in the installTFpython function.
• The installTFpython function now installs python 3.8 by default.

SpatialDDLS 1.0.3 (2024-10-28)

• SingleCellExperiment adds a saveRDS S3 generics in the new BioC version. To avoid incompatibilities, it is not completely loaded anymore.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.