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