Available Documentation
oncoplot
merge_oncoplot_params
OncoplotResult
prepare_oncoplot_data
identify_top_genes
score_sample_by_gene_rank
rank_genes_by_pathway
prettify
_IO
save_dataset
make_df_obs_adataX
include_obs
_column_plots
barh_column
l2fc_dotplot_single
l2fc_dotplot_column
barh_l2fc_dotplot_column
_corr_dotplots
corr_dotplot
corr_dotplot_dev
spearman_cor_dotplot
DataFrame
_datapoints
datapoints
_diff_test
_expectation_based_covar_correction
calculate_expectations
model_spec
predict_expectation
regress_out
excess_expectation
convert_ols_summary_to_expectation_df
reconstruct_expectation_model_spec
_histograms
adata_histograms
_metab_IO
AnnData
_model_fit
*_wide(...)
adata.uns
_paired_datapoints
paired_datapoints
ref_vs_target_adata()
_plots
volcano_plot_generic
qqplot
timeseries_paired_datapoints
_plots_depreciated
_preprocessing
ref_vs_target_adata
_row_plots
plot_columns
_simulate_data
sim_observations_covars
sim_covar_dependent_features
sim_covar_dependent_dataset
_somascan_IO
read_adat_2_AnnData
soma_fill_sampletype_obs_values
soma_make_adata_index_unique_by_merge
make_df_obs_adataX_soma
_utils
show_tol_colors
show_colors
_venn_plots
venn_plot_2list
venn_plot_3list
geneset_enrichment_venn
geneset_enrichemnt_ol_ven_M_n_N_x
palettes
reset_cellxgene_var_names
downcast_layers_to_float32
annotate_QC_genes
calculate_qc_metrics
plot_QC_metrics_scatter
plot_QC_metrics_violin
plot_qc_metrics
annotate_n_view_adata_raw_counts
basic_filitering
filter_cells_by_anotated_QC_gene
remove_genes
process2scaledPCA
norm_log
HVG_selection_log_norm_seurat
HVG_selection_log_norm_seurat_v3
HVG_removal
regress_out_anotated_QC_genes
scale_func
PCA_func
calc_cell_cycle_score
regress_cell_cycle_score_func
leiden_clustering
rename_leiden_clusters
leiden_cluster_sil_score
silhouette_walk_Largest_drop
silhouette_walk_4_Largest_drops
silhouette_score_n_plot
silhouette_score_of_obs_key_n_plot
plot_batch_obs_key_of_obs_key2
plot_adata_row_total_dist
plot_adata_raw_and_X_rowdist_old
plot_adata_raw_and_X_rowdist
plot_batch_obs_key_of_obs_key2_old
plot_percent_obs_key2_per_batch_obs_key
ingest_verbose
Ingest
DATASET_class
sctl.pp
sctl.pl
sctl.tl