Man pages for protti
Bottom-Up Proteomics and LiP-MS Quality Control and Data Analysis Tools
| analyse_functional_network | Analyse protein interaction network for significant hits |
| anova_protti | Perform ANOVA |
| assign_missingness | Assignment of missingness types |
| assign_peptide_type | Assign peptide type |
| barcode_plot | Barcode plot |
| calculate_aa_scores | Calculate scores for each amino acid position in a protein... |
| calculate_diff_abundance | Calculate differential abundance between conditions |
| calculate_go_enrichment | Perform gene ontology enrichment analysis |
| calculate_imputation | Sampling of values for imputation |
| calculate_kegg_enrichment | Perform KEGG pathway enrichment analysis |
| calculate_protein_abundance | Label-free protein quantification |
| calculate_sequence_coverage | Protein sequence coverage |
| calculate_treatment_enrichment | Check treatment enrichment |
| create_queue | Creates a mass spectrometer queue for Xcalibur |
| create_structure_contact_map | Creates a contact map of all atoms from a structure file |
| create_synthetic_data | Creates a synthetic limited proteolysis proteomics dataset |
| diff_abundance | Calculate differential abundance between conditions |
| drc_4p | Dose response curve helper function |
| drc_4p_plot | Plotting of four-parameter dose response curves |
| extract_metal_binders | Extract metal-binding protein information from UniProt |
| fetch_alphafold_aligned_error | Fetch AlphaFold aligned error |
| fetch_alphafold_prediction | Fetch AlphaFold prediction |
| fetch_chebi | Fetch ChEBI database information |
| fetch_eco | Fetch evidence & conclusion ontology |
| fetch_go | Fetch gene ontology information from geneontology.org |
| fetch_kegg | Fetch KEGG pathway data from KEGG |
| fetch_metal_pdb | Fetch structural information about protein-metal binding from... |
| fetch_mobidb | Fetch protein disorder and mobility information from MobiDB |
| fetch_pdb | Fetch structure information from RCSB |
| fetch_pdb_structure | Fetch PDB structure atom data from RCSB |
| fetch_quickgo | Fetch information from the QuickGO API |
| fetch_uniprot | Fetch protein data from UniProt |
| fetch_uniprot_proteome | Fetch proteome data from UniProt |
| filter_cv | Data filtering based on coefficients of variation (CV) |
| find_all_subs | Find all sub IDs of an ID in a network |
| find_chebis | Find ChEBI IDs for name patterns |
| find_peptide | Find peptide location |
| find_peptide_in_structure | Finds peptide positions in a PDB structure based on... |
| fit_drc_4p | Fitting four-parameter dose response curves |
| go_enrichment | Perform gene ontology enrichment analysis |
| impute | Imputation of missing values |
| kegg_enrichment | Perform KEGG pathway enrichment analysis |
| map_peptides_on_structure | Maps peptides onto a PDB structure or AlphaFold prediction |
| median_normalisation | Intensity normalisation |
| metal_chebi_uniprot | List of metal-related ChEBI IDs in UniProt |
| metal_go_slim_subset | Molecular function gene ontology metal subset |
| metal_list | List of metals |
| network_analysis | Analyse protein interaction network for significant hits |
| normalise | Intensity normalisation |
| parallel_create_structure_contact_map | Creates a contact map of all atoms from a structure file... |
| parallel_fit_drc_4p | Fitting four-parameter dose response curves (using parallel... |
| peptide_profile_plot | Peptide abundance profile plot |
| peptide_type | Assign peptide type |
| plot_drc_4p | Perform gene ontology enrichment analysis |
| plot_peptide_profiles | Peptide abundance profile plot |
| plot_pval_distribution | Plot histogram of p-value distribution |
| predict_alphafold_domain | Predict protein domains of AlphaFold predictions |
| protti_colours | Colour scheme for protti |
| ptsi_pgk | Structural analysis example data |
| pval_distribution_plot | Plot histogram of p-value distribution |
| qc_charge_states | Check charge state distribution |
| qc_contaminants | Percentage of contaminants per sample |
| qc_cvs | Check CV distribution |
| qc_data_completeness | Data completeness |
| qc_ids | Check number of precursor, peptide or protein IDs |
| qc_intensity_distribution | Check intensity distribution per sample and overall |
| qc_median_intensities | Median run intensities |
| qc_missed_cleavages | Check missed cleavages |
| qc_pca | Plot principal component analysis |
| qc_peak_width | Peak width over retention time |
| qc_peptide_type | Check peptide type percentage share |
| qc_proteome_coverage | Proteome coverage per sample and total |
| qc_ranked_intensities | Check ranked intensities |
| qc_sample_correlation | Correlation based hirachical clustering of samples |
| qc_sequence_coverage | Protein coverage distribution |
| randomise_queue | Randomise samples in MS queue |
| rapamycin_10uM | Rapamycin 10 uM example data |
| rapamycin_dose_response | Rapamycin dose response example data |
| read_protti | Read, clean and convert |
| replace_identified_by_x | Replace identified positions in protein sequence by "x" |
| scale_protti | Scaling a vector |
| sequence_coverage | Protein sequence coverage |
| split_metal_name | Convert metal names to search pattern |
| treatment_enrichment | Check treatment enrichment |
| try_query | Query from URL |
| ttest_protti | Perform Welch's t-test |
| viridis_colours | Viridis colour scheme |
| volcano_plot | Volcano plot |
| volcano_protti | Volcano plot |
| woods_plot | Woods' plot |
