az7jh2/SDePER: SDePER v1.4.0

Updates:

• Added single cell augmentation feature for scRNA-seq reference data.

• Implemented failure steps for handling irregular $\theta$ values after optimization.

• Added support for transferring cell type proportions based on PCA or UMAP embeddings of latent space, or directly on the original latent space in cell type proportion prediction using CVAE.

• Introduced caching in GLRM to accelerate computations by storing calculated likelihood values, reducing duplicate calculations. Note: This feature is disabled by default due to potential optimization failures caused by unknown reasons (#5).

Bug Fixes:

• Resolved issue with spot name inconsistencies when spots are filtered out if cell type proportions predicted by CVAE were used for $\theta$ initialization in GLRM modeling.

• Fixed bug causing errors when plotting CVAE loss during training in the absence of validation data.