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Main
Intuitions behind clone2vec
Tutorial
API
c2v.datasets.Weinreb_in_vitro
c2v.datasets.Erickson_murine_development
c2v.datasets.Liu_NSCLC_CD8
c2v.pp.clones_adata
c2v.pp.make_unique_clones
c2v.pp.recalc_composition
c2v.pp.transfer_annotation
c2v.pp.transfer_expression
c2v.tl.clonal_nn
c2v.tl.clonocluster
c2v.tl.smooth
c2v.tl.group_connectivity
c2v.tl.clone2vec
c2v.tl.clone2vec_Poi
c2v.tl.project_clone2vec
c2v.tl.project_clone2vec_Poi
c2v.tl.find_mnn
c2v.tl.align
c2v.tl.associations
c2v.tl.graph_associations
c2v.tl.eigenvalue_test
c2v.tl.catboost
c2v.utils.stack_layers
c2v.utils.correct_shap
c2v.utils.connect_clones
c2v.utils.get_connectivity_matrix
c2v.utils.regress_categories
c2v.utils.impute
c2v.utils.gs
c2v.utils.laplacian_eigenmaps
c2v.pl.group_scatter
c2v.pl.group_kde
c2v.pl.loss_history
c2v.pl.clone_size
c2v.pl.nesting_clones
c2v.pl.volcano
c2v.pl.shap_volcano
c2v.pl.barplot
c2v.pl.heatmap
c2v.pl.predictors_comparison
c2v.pl.catboost_perfomance
c2v.pl.clones2cells
c2v.pl.graph
c2v.pl.group_connectivity
c2v.pl.pca_loadings
c2v.pl.scaled_dotplot
c2v.pl.scatter2vars
c2v.pl.embedding_axis
c2v.pl.small_cbar
c2v.pl.fancy_legend
c2v.seurat.read
c2v.seurat.integrate_data
Examples
Introduction to clonal embeddings
Fast clonal embeddings construction with
py-fastglmpca
Archetypal analysis of clonal embeddings
Graph input for clonal embeddings construction
Batch effect in clonal embeddings
Integration (alignment) of clonal embeddings
Beyond clonal data: spatial clustering of genes
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