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Installation
Usage Principles
API
scanpy-GPU
rapids_singlecell.pp.calculate_qc_metrics
rapids_singlecell.pp.filter_cells
rapids_singlecell.pp.filter_genes
rapids_singlecell.pp.normalize_total
rapids_singlecell.pp.log1p
rapids_singlecell.pp.highly_variable_genes
rapids_singlecell.pp.regress_out
rapids_singlecell.pp.scale
rapids_singlecell.pp.pca
rapids_singlecell.pp.normalize_pearson_residuals
rapids_singlecell.pp.flag_gene_family
rapids_singlecell.pp.filter_highly_variable
rapids_singlecell.pp.harmony_integrate
rapids_singlecell.pp.scrublet
rapids_singlecell.pp.scrublet_simulate_doublets
rapids_singlecell.pp.neighbors
rapids_singlecell.tl.umap
rapids_singlecell.tl.tsne
rapids_singlecell.tl.diffmap
rapids_singlecell.tl.draw_graph
rapids_singlecell.tl.mde
rapids_singlecell.tl.embedding_density
rapids_singlecell.tl.louvain
rapids_singlecell.tl.leiden
rapids_singlecell.tl.rank_genes_groups_logreg
squidpy-GPU:
gr
rapids_singlecell.gr.spatial_autocorr
rapids_singlecell.gr.ligrec
decoupler-GPU:
dcg
rapids_singlecell.dcg.run_mlm
rapids_singlecell.dcg.run_wsum
Get object from
AnnData
:
get
rapids_singlecell.get.aggregate
rapids_singlecell.get.anndata_to_GPU
rapids_singlecell.get.anndata_to_CPU
Memory Management
Release notes
References
Notebooks
Demo Workflow & Decoupler
HVG:seurat_v3 & harmony workflow
Pearson Residues Example
1 Million Brain Cells
Spatial Autocorrelation
Ligrec Benchmark
Acknowledgements
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