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grassp 0.1 documentation - Home grassp 0.1 documentation - Home
  • 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
  • .md

API

API#

Import grassp as:

import grassp as gr
  • Preprocessing: pp
    • Basic Preprocessing
    • Enrichment
    • Imputation
    • Annotation
  • Tools: tl
    • Clustering
    • Cluster Merging
    • Semi-supervised Localization
    • Ontology-aware Annotation
    • Ontology Enrichment
    • Model-based Gene Set Analysis
    • C-COMPASS
    • Integration
    • Graph analysis
  • Plotting: pl
    • Preprocessing
    • Embedding
    • Integration
    • Clustering
    • Ternary
  • IO: io
    • Search Engine Outputs
    • Other Formats
    • pRoloc interoperability
  • Datasets
    • Public Datasets
    • Unpublished Datasets
    • Data Portal
    • Metadata

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pRoloc integration: for pRoloc users

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Preprocessing: pp

By Max Frank

© Copyright 2025, Max Frank.