Index A | B | C | D | E | F | G | H | I | L | M | N | P | R | S | T | V A add_legend_to_axes() (in module alphapepttools.pl) add_legend_to_axes_from_patches() (in module alphapepttools.pl) add_lines() (in module alphapepttools.pl) add_metadata() (in module alphapepttools.pp) alphapepttools.data module alphapepttools.io module alphapepttools.metrics module alphapepttools.pl module alphapepttools.pp module alphapepttools.tl module AnnDataFactory (class in alphapepttools.io) available_data() (in module alphapepttools.data) B barplot() (in module alphapepttools.pl) BaseColormaps (class in alphapepttools.pl) BaseColors (class in alphapepttools.pl) BasePalettes (class in alphapepttools.pl) boxplot() (in module alphapepttools.pl) bpca() (in module alphapepttools.tl) C calculate_qc_metrics() (in module alphapepttools.metrics) coefficient_of_variation() (in module alphapepttools.metrics) copy_with() (alphapepttools.pl.PlotConfig method) create_anndata() (alphapepttools.io.AnnDataFactory method) create_figure() (in module alphapepttools.pl) D data (alphapepttools.pl.PlotConfig attribute) default_colormaps (alphapepttools.pl.BaseColormaps attribute) default_colors (alphapepttools.pl.BaseColors attribute) default_palettes (alphapepttools.pl.BasePalettes attribute), [1] detect_special_values() (in module alphapepttools.pp) diff_exp_alphaquant() (in module alphapepttools.tl) diff_exp_ebayes() (in module alphapepttools.tl) diff_exp_ttest() (in module alphapepttools.tl) drop_singleton_batches() (in module alphapepttools.pp) E extract_pca_anndata() (in module alphapepttools.tl) F filter_by_metadata() (in module alphapepttools.pp) filter_data_completeness() (in module alphapepttools.pp) fit_transform() (alphapepttools.pl.MappedColormaps method) fraction_complete() (in module alphapepttools.metrics) from_files() (alphapepttools.io.AnnDataFactory class method) G get() (alphapepttools.pl.BaseColormaps class method) (alphapepttools.pl.BaseColors class method) (alphapepttools.pl.BasePalettes class method) get_color_mapping() (in module alphapepttools.pl) get_data() (in module alphapepttools.data) get_id2gene_map() (in module alphapepttools.tl) H histogram() (in module alphapepttools.pl) I impute_bpca() (in module alphapepttools.pp) impute_gaussian() (in module alphapepttools.pp) impute_knn() (in module alphapepttools.pp) impute_median() (in module alphapepttools.pp) L label_axes() (in module alphapepttools.pl) label_plot() (in module alphapepttools.pl) layered_plot() (in module alphapepttools.pl) list_available_reader() (in module alphapepttools.io) M make_scatter_config() (in module alphapepttools.pl) map_genes_to_protein_groups() (in module alphapepttools.tl) MappedColormaps (class in alphapepttools.pl) module alphapepttools.data alphapepttools.io alphapepttools.metrics alphapepttools.pl alphapepttools.pp alphapepttools.tl N nan_safe_bh_correction() (in module alphapepttools.tl) nan_safe_ttest_ind() (in module alphapepttools.tl) nanlog() (in module alphapepttools.pp) normalize() (in module alphapepttools.pp) number_detected() (in module alphapepttools.metrics) P pca() (in module alphapepttools.tl) plot_pca() (in module alphapepttools.pl) plot_pca_loadings() (in module alphapepttools.pl) plot_pca_loadings_2d() (in module alphapepttools.pl) PlotConfig (class in alphapepttools.pl) Plots (class in alphapepttools.pl) pooled_coefficient_of_variation() (in module alphapepttools.metrics) pooled_median_absolute_deviation() (in module alphapepttools.metrics) prepare_pca_1d_loadings_data_to_plot() (in module alphapepttools.tl) prepare_pca_2d_loadings_data_to_plot() (in module alphapepttools.tl) prepare_scree_data_to_plot() (in module alphapepttools.tl) principal_component_regression() (in module alphapepttools.metrics) R rank_median_plot() (in module alphapepttools.pl) read_pg_table() (in module alphapepttools.io) read_psm_table() (in module alphapepttools.io) S save_figure() (in module alphapepttools.pl) scalar_mappable (alphapepttools.pl.MappedColormaps attribute) scale_and_center() (in module alphapepttools.pp) scanpy_pycombat() (in module alphapepttools.pp) scatter() (in module alphapepttools.pl) scree_plot() (in module alphapepttools.pl) show_rgba_color_list() (in module alphapepttools.pl) T to_kwargs() (alphapepttools.pl.PlotConfig method) total_intensity() (in module alphapepttools.metrics) V violinplot() (in module alphapepttools.pl) volcano() (in module alphapepttools.pl)