SPACEL: characterizing spatial transcriptome architectures by deep-learning SPACEL (SP atial A rchitecture C haracterization by d E ep L earning) is a Python package of deep-learning-based …

To install SPACEL, you need to install PyTorch with GPU support first. If you don’t need GPU acceleration, you can just skip the installation for cudnn and cudatoolkit.

SPACEL workflow (2/3): Identification of spatial domain by Splane on mouse brain ST dataset SPACEL workflow (3/3): Alignment 3D tissue by Scube on mouse brain ST dataset

API Edit on GitHubAPI Spoint:

Tutorials SPACEL workflow (1/3): Deconvolution by Spoint on mouse brain ST dataset Edit on GitHub

Tutorials SPACEL workflow (2/3): Identification of spatial domain by Splane on mouse brain ST dataset Edit on GitHub

SPACEL.Spoint.model.init_model(sc_ad, st_ad, celltype_key, sc_genes=None, st_genes=None, used_genes=None, deg_method='wilcoxon', n_top_markers=200, n_top_hvg=None, log2fc_min=0.5, …

SPACEL.Splane.model.init_model(expr_ad_list, n_clusters, k=2, use_weight=True, train_prop=0.5, n_neighbors=6, min_prop=0.01, lr=0.003, l1=0.01, l2=0.01, latent_dim=16, hidden_dims=64, …

Splane tutorial: Identification of uniform spatial domain on human breast cancer Visium dataset July 2023 Dataset: 11 Visium slices of human breast cancer (here).

Scube tutorial: Alignment of consecutive ST slices on mouse embryo Stereo-seq dataset July 2023 Dataset: 13 ST slices of mouse embryos (here)