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Installation
Tutorials
Grassp Centrifugation Workflow Tutorial
Dataset integration
API
Preprocessing:
pp
grassp.pp.calculate_qc_metrics
grassp.pp.filter_samples
grassp.pp.filter_proteins
grassp.pp.highly_variable_proteins
grassp.pp.filter_proteins_per_replicate
grassp.pp.aggregate_proteins
grassp.pp.aggregate_samples
grassp.pp.normalize_total
grassp.pp.drop_excess_MQ_metadata
grassp.pp.remove_contaminants
grassp.pp.filter_min_consecutive_fractions
grassp.pp.calculate_enrichment_vs_untagged
grassp.pp.calculate_enrichment_vs_all
grassp.pp.impute_gaussian
Tools:
tl
grassp.tl.leiden_mito_sweep
grassp.tl.knn_annotation
grassp.tl.calculate_interfacialness_score
grassp.tl.silhouette_score
grassp.tl.calinski_habarasz_score
grassp.tl.tagm_map_train
grassp.tl.tagm_map_predict
grassp.tl.calculate_cluster_enrichment
grassp.tl.align_adatas
grassp.tl.aligned_umap
grassp.tl.remodeling_score
grassp.tl.to_knn_graph
grassp.tl.get_n_nearest_neighbors
Plotting:
pl
grassp.pl.highly_variable_proteins
grassp.pl.bait_volcano_plots
grassp.pl.protein_clustermap
grassp.pl.sample_heatmap
grassp.pl.aligned_umap
grassp.pl.remodeling_score
grassp.pl.remodeling_sankey
grassp.pl.mr_plot
grassp.pl.qsep_heatmap
grassp.pl.qsep_boxplot
grassp.pl.tagm_map_contours
grassp.pl.tagm_map_pca_ellipses
grassp.pl.ternary
IO
Datasets
grassp.ds.hein_2024
grassp.ds.itzhak_2016
grassp.ds.schessner_2023
grassp.ds.hek_dc_2025
grassp.ds.hek_atps_2025
Contributors
References
.md
.pdf
IO
IO
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