API¶
sccloud can also be used as a python package. Import sccloud by:
import sccloud as scc
Analysis Tools¶
Read and Write¶
read_input |
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write_output |
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aggregate_matrices |
Preprocess¶
qc_metrics |
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get_filter_stats |
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filter_data |
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select_features |
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log_norm |
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highly_variable_features |
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pca |
Batch Correction¶
set_group_attribute |
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correct_batch |
Nearest Neighbors¶
neighbors |
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calc_kBET |
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calc_kSIM |
Diffusion Map¶
diffmap |
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reduce_diffmap_to_3d |
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calc_pseudotime |
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infer_path |
Cluster algorithms¶
louvain |
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leiden |
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spectral_louvain |
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spectral_leiden |
Visualization Algorithms¶
tsne |
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fitsne |
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umap |
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fle |
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net_tsne |
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net_fitsne |
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net_umap |
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net_fle |
Differential Expression Analysis¶
de_analysis |
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markers |
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find_markers |
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write_results_to_excel |
Write single-cell-portal-formatted outputs¶
tools.run_scp_output |
Annotate clusters:¶
infer_cell_types |
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annotate |
Plotting¶
Interactive Plots¶
embedding |
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composition_plot |
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variable_feature_plot |
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heatmap |
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dotplot |
Quality Control Plots¶
violin |
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scatter |
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scatter_matrix |
Demultiplexing¶
estimate_background_probs |
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demultiplex |
Miscellaneous¶
search_genes |
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search_de_genes |