Setup & Usage
Tutorials
API
fetch_human_atlas()
fetch_mouse_atlas()
get_region_phenotypes()
SpeciesTrans
SpeciesTrans.atlas_type
SpeciesTrans.regions
SpeciesTrans.embeddings
SpeciesTrans._load_embeddings()
SpeciesTrans._dual_mapping()
SpeciesTrans._translate()
SpeciesTrans.mouse_to_human()
SpeciesTrans.human_to_mouse()
map_phenotype_to_nifti()
plot_mouse_phenotype()
plot_human_phenotype()
plot_surface_phenotype()
Preprocess_Sn
Preprocess_Sn.dataset_qc()
Preprocess_Sn.dataset_normalized()
Preprocess_Sn.dataset_common_genes()
Preprocess_Sn.dataset_batch_correct()
Preprocess_Sn.dataset_smooth()
Preprocess_Sn.dataset_scaled()
Preprocess_Sn.preprocess_pipeline()
stable_gene_filter()
calculate_thresholds()
DataIntegrator
DataIntegrator.__init__()
DataIntegrator.run()
DataIntegrator.pool_construction()
DataIntegrator.clean_pool()
DataIntegrator.weighted_average()
DataIntegrator.downsample_data()
DataIntegrator.generate_integrated_anndata()
calculate_rank()
transform_human_mouse()
independent_test()
DnnPipeline
DnnPipeline.cfg
DnnPipeline.logger
DnnPipeline.execute()
DnnPipeline.train()
DnnPipeline.trans()
DnnPipeline.test()
DnnPipeline._process_single_dataset()
DnnPipeline._train_single_model()
generate_embeddings()
Other
Here are some functions used in the development of TransBrain. The code is available in our GitHub repository.