API

Input/Output

io.write_deseq_tables(pb, samplesheet_path, ...)

Save AnnData as counts matrix and samplesheet as read by the DESeq2 script.

Preprocessing

pp.is_outlier(adata, metric_col, *[, ...])	Detect outliers by median absolute deviation (MAD).
pp.validate_obs(adata_obs, ref_meta_dict[, ...])	Validates the metadata in the adata.obs or a pandas DataFrame against a reference metadata dictionary.

Tools

tl.fdr_correction(df[, pvalue_col, ...])	Adjust p-values in a data frame with test results using FDR correction.
tl.scissor_wilcoxon_test(df[, pos_col, neg_col])	Tests if the fractions of scissor+ cells is significantly different from the fraction of scissor- cells.
tl.CpdbAnalysis(cpdb, adata, *, ...[, min_obs])	Class that handles comparative cellphonedb analysis.
tl.long_form_df_to_decoupler(df, *[, ...])	Convert a long-form data frame of DE results into a pair of logFC/pvalue matrices as used by decoupler.

Plotting

pl.reshape_clustermap(cmap[, cell_width, ...])	Resizes the components of a seaborn clustermap object to match the specified cell widths and heights.
pl.save_fig_mfmt(fig, res_dir, filename[, fmt])	Save a matplotlib or altair figure in the specified format(s) to the given directory with the given filename.
pl.significance_heatmap(df[, p_cutoff, ...])	Plot a results data frame of a comparison as a heatmap.
pl.plot_paired(adata, groupby, *[, ...])	Pairwise expression plot.Makes on panel with a paired scatterplot for each variable.