NEWS.md

In SpatialDDLS: Deconvolution of Spatial Transcriptomics Data Based on Neural Networks

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.

SpatialDDLS documentation built on Oct. 31, 2024, 5:07 p.m.