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alphapepttools
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.impute_gaussian
alphapepttools.pp.impute_median
alphapepttools.pp.impute_knn
alphapepttools.pp.impute_bpca
alphapepttools.pp.scanpy_pycombat
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.pca
alphapepttools.tl.bpca
alphapepttools.tl.diff_exp_ebayes
alphapepttools.metrics.coefficient_of_variation
alphapepttools.metrics.principal_component_regression
alphapepttools.metrics.pooled_coefficient_of_variation
alphapepttools.metrics.pooled_median_absolute_deviation
alphapepttools.pl.Plots
alphapepttools.pl.add_lines
alphapepttools.pl.label_plot
alphapepttools.pl.BaseColormaps
alphapepttools.pl.BaseColors
alphapepttools.pl.BasePalettes
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.io.read_psm_table
alphapepttools.io.read_pg_table
alphapepttools.io.AnnDataFactory
alphapepttools.io.list_available_reader
alphapepttools.data.available_data
alphapepttools.data.get_data
Tutorials
Bader et al, 2020: Analysis of body fluid proteomics
Li et al, 2025: Analysis of peptidomics data (PELSA)
Stadler et al, 2025: Analysis of bulk proteomics data
Introduction to proteomics data analysis with
anndata
Example
alphapepttools
workflow with proteomics data
Scientific visualizations with
alphapepttools
Principal component analysis
Filtering by metadata
Changelog
Contributing guide
References
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