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SDePER v1.3.0
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@az7jh2 az7jh2 released this 09 May 04:09
· 2 commits to main since this release
v1.3.0
9fb9e7a

Updates:

  • Introduced prediction of cell type proportions utilizing the CVAE latent space. Currently, the proportions are transferred from the scRNA-seq condition to the spatial condition in latent space. Then the predicted cell type proportions are used as initial value of $\theta$ for GLRM modeling (#13).

  • Reused $\theta$ and $e^{\alpha}$ estimations from stage 1 of GLRM modeling for initializing stage 2 (#12).

  • Increased the weight of spatial spots and scRNA-seq cells in CVAE training against generated pseudo-spots.

  • Added support for retaining only highly variable genes in the spatial data. By default all genes are retained.

  • SDePER options are written to a text file within the diagnosis folder, and only DE genes are retained in the CVAE-transformed data during saving if command-line option --redo_de is true.

  • Decreased the default number of command-line option --n_pseudo_spot to 100,000.

Bug Fixes:

  • Resolved a bug where errors occurred during diagnostic UMAP drawing if only cell type markers were provided, and no scRNA-seq cells were available.
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