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alphapepttools
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API
alphapepttools.pp.add_metadata
alphapepttools.pp.filter_by_metadata
alphapepttools.pp.filter_data_completeness
alphapepttools.pp.scale_and_center
alphapepttools.pp.nanlog
alphapepttools.pp.detect_special_values
alphapepttools.pp.normalize
alphapepttools.pp.irs
alphapepttools.pp.impute_gaussian
alphapepttools.pp.impute_median
alphapepttools.pp.impute_knn
alphapepttools.pp.impute_bpca
alphapepttools.pp.scanpy_pycombat
alphapepttools.pp.drop_singleton_batches
alphapepttools.tl.get_id2gene_map
alphapepttools.tl.map_genes_to_protein_groups
alphapepttools.tl.nan_safe_bh_correction
alphapepttools.tl.nan_safe_ttest_ind
alphapepttools.tl.diff_exp_ttest
alphapepttools.tl.diff_exp_alphaquant
alphapepttools.tl.diff_exp_ebayes
alphapepttools.tl.pca
alphapepttools.tl.bpca
alphapepttools.tl.extract_pca_anndata
alphapepttools.tl.prepare_pca_1d_loadings_data_to_plot
alphapepttools.tl.prepare_pca_2d_loadings_data_to_plot
alphapepttools.tl.prepare_scree_data_to_plot
alphapepttools.metrics.coefficient_of_variation
alphapepttools.metrics.principal_component_regression
alphapepttools.metrics.pooled_coefficient_of_variation
alphapepttools.metrics.pooled_median_absolute_deviation
alphapepttools.metrics.calculate_qc_metrics
alphapepttools.metrics.fraction_complete
alphapepttools.metrics.number_detected
alphapepttools.metrics.total_intensity
alphapepttools.pl.Plots
alphapepttools.pl.add_lines
alphapepttools.pl.label_plot
alphapepttools.pl.BaseColormaps
alphapepttools.pl.BaseColors
alphapepttools.pl.BasePalettes
alphapepttools.pl.MappedColormaps
alphapepttools.pl.show_rgba_color_list
alphapepttools.pl.PlotConfig
alphapepttools.pl.make_scatter_config
alphapepttools.pl.add_legend_to_axes
alphapepttools.pl.add_legend_to_axes_from_patches
alphapepttools.pl.create_figure
alphapepttools.pl.label_axes
alphapepttools.pl.save_figure
alphapepttools.pl.get_color_mapping
alphapepttools.pl.layered_plot
alphapepttools.pl.histogram
alphapepttools.pl.scatter
alphapepttools.pl.barplot
alphapepttools.pl.boxplot
alphapepttools.pl.violinplot
alphapepttools.pl.rank_median_plot
alphapepttools.pl.plot_pca
alphapepttools.pl.scree_plot
alphapepttools.pl.plot_pca_loadings
alphapepttools.pl.plot_pca_loadings_2d
alphapepttools.pl.volcano
alphapepttools.io.read_psm_table
alphapepttools.io.read_pg_table
alphapepttools.io.AnnDataFactory
alphapepttools.io.mulink_from_anndatas
alphapepttools.io.list_available_reader
alphapepttools.data.available_data
alphapepttools.data.get_data
Tutorials
Bader et al, 2020: Analysis of body fluid proteomics
Analysis of PELSA peptidomics data (Li et al, 2025)
Stadler et al, 2025: Analysis of bulk proteomics data
Weiss et al, 2026: Single-cell spatial proteomics on human liver zonation
Lehtiö et al., 2021: Multimodal data integration
Introduction to proteomics data analysis with
anndata
Example
alphapepttools
workflow with proteomics data
Scientific visualizations with
alphapepttools
Principal component analysis
Volcanoplot
TMT data normalization
Scalability of anndata x alphapepttools
Filtering by metadata
Changelog
Contributing guide
References
System Settings
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