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Installation
Tutorials
Differential Centrifugation (DC) Workflow
Organellar Immunoprecipitation (OrgIP) Workflow
Dataset integration
Predicting subcellular compartments with C-COMPASS
Ontology-aware annotation with “independent_diffusion”
pRoloc integration: for grassp users
pRoloc integration: for pRoloc users
API
Preprocessing:
pp
grassp.pp.calculate_qc_metrics
grassp.pp.calculate_replicate_cv
grassp.pp.neighbors
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.remove_cRAP_proteins
grassp.pp.filter_min_consecutive_fractions
grassp.pp.calculate_enrichment_vs_untagged
grassp.pp.calculate_enrichment_vs_all
grassp.pp.impute_gaussian
grassp.pp.impute_knn
grassp.pp.add_markers
grassp.pp.add_external_validation_markers
grassp.pp.annotate_uniprot_cc
grassp.pp.set_sensible_compartment_colors
Tools:
tl
grassp.tl.leiden_mito_sweep
grassp.tl.markov_clustering
grassp.tl.calculate_interfacialness_score
grassp.tl.silhouette_score
grassp.tl.calinski_habarasz_score
grassp.tl.qsep_score
grassp.tl.tagm_map_train
grassp.tl.tagm_map_predict
grassp.tl.knn_f1_score
grassp.tl.class_balance
grassp.tl.merge_clusters_go
grassp.tl.merge_small_clusters
grassp.tl.paga_dendrogram
grassp.tl.dendrogram_cherry_pairs
grassp.tl.competitive_propagation
grassp.tl.knn_annotation
grassp.tl.soft_cluster_annotation
grassp.tl.resolve_soft_labels
grassp.tl.svm_train
grassp.tl.svm_annotation
grassp.tl.independent_diffusion
grassp.tl.resolve_diffusion
grassp.tl.calculate_cluster_enrichment
grassp.tl.enrichment_to_cluster_distribution
grassp.tl.mgsa
grassp.tl.calculate_mgsa
grassp.tl.mgsa_to_cluster_distribution
grassp.tl.MgsaResult
grassp.tl.load_gmt
grassp.tl.ccompass
grassp.tl.ccompass_default_params
grassp.tl.align_adatas
grassp.tl.aligned_umap
grassp.tl.remodeling_score
grassp.tl.mr_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.marker_profiles
grassp.pl.marker_profiles_split
grassp.pl.protein_clustermap
grassp.pl.sample_heatmap
grassp.pl.embedding_prob
grassp.pl.umap_prob
grassp.pl.pca_prob
grassp.pl.tsne_prob
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.knn_violin
grassp.pl.ternary
IO:
io
grassp.io.read_maxquant
grassp.io.read_diann
grassp.io.read_fragpipe
grassp.io.read_prolocdata
Datasets
grassp.ds.hein_2024
grassp.ds.itzhak_2016
grassp.ds.schessner_2023
grassp.ds.hek_dc_2025
grassp.ds.hek_atps_2025
grassp.ds.load_dataset
grassp.ds.list_prolocdata_files
grassp.ds.download_prolocdata
grassp.ds.uniprot_compartment_goterms
Contributing
Contributors
Changelog
References
System Settings
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