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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.scanpy_pycombat
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.diff_exp_ebayes
alphapepttools.metrics.principal_component_regression
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
Introduction to proteomics data analysis with
anndata
Example
alphapepttools
workflow with proteomics data
Basic alphapepttools workflow
Batch correction (Reanalysis of Stadler et al, 2025)
Tutorial: Reading PSM tables into AnnData format
Plotting
Changelog
Contributing guide
References
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