API¶
scCloud
can also be used as a python package. Import scCloud
by:
import scCloud
Tools:¶
Aggregate channel-specific count matrices
tools.aggregate_10x_matrices |
Preprocess
tools.read_input |
|
tools.update_var_names |
|
tools.filter_data |
|
tools.log_norm |
|
tools.run_pca |
|
tools.run_rpca |
|
tools.get_anndata_for_subclustering |
|
tools.filter_cells_cite_seq |
Batch correction
tools.set_group_attribute |
|
tools.estimate_adjustment_matrices |
|
tools.filter_genes_dispersion |
|
tools.collect_variable_gene_matrix |
|
tools.correct_batch_effects |
Diffusion map
tools.run_diffmap |
|
tools.run_pseudotime_calculation |
Cluster algorithms
tools.run_louvain |
|
tools.run_kmeans |
|
tools.run_approximated_louvain |
Visualization algorithms
tools.run_tsne |
|
tools.run_fitsne |
|
tools.run_umap |
|
tools.run_force_directed_layout |
Differential expression analysis
tools.run_de_analysis |
Write single-cell-portal-formatted outputs
tools.run_scp_output |
Annotate clusters:¶
annotate_cluster.annotate_clusters |
|
annotate_cluster.annotate_anndata_object |
Plotting:¶
Static plots
plotting.plot_composition |
|
plotting.plot_scatter |
|
plotting.plot_scatter_groups |
|
plotting.plot_scatter_genes |
|
plotting.plot_scatter_gene_groups |
|
plotting.plot_heatmap |
Interactive plots
plotting.scatter |
|
plotting.scatter_real |
|
plotting.scatter3d |
|
plotting.scatter3d_real |
Quality control plots
plotting.plot_qc_violin |
DemuxEM:¶
Estimation
demuxEM.estimate_background_probs |
|
demuxEM.demultiplex |
|
demuxEM.down_sampling |
Plotting
demuxEM.plot_adt_hist |
|
demuxEM.plot_rna_hist |
|
demuxEM.plot_bar |
|
demuxEM.plot_violin |
|
demuxEM.plot_heatmap |
|
demuxEM.plot_dataframe_bar |
|
demuxEM.plot_down_sampling |
CITE-Seq:¶
cite_seq.merge_rna_and_adt_data |
Miscellaneous:¶
misc.search_genes |
|
misc.search_de_genes |