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 sequence
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
correct_lip_for_abundance
                        Protein abundance correction for LiP-data
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
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_interpro          Fetch domain and residue information from
                        InterPro
fetch_kegg              Fetch KEGG pathway data from KEGG
fetch_metal_pdb         Fetch structural information about
                        protein-metal binding from MetalPDB
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 positional matching
fit_drc_4p              Fitting four-parameter dose response curves
impute                  Imputation of missing values
impute_randomforest     Imputation of Missing Values Using Random
                        Forest Imputation
mako_colours            Viridis colour scheme
map_peptides_on_structure
                        Maps peptides onto a PDB structure or AlphaFold
                        prediction
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
normalise               Intensity normalisation
parallel_create_structure_contact_map
                        Creates a contact map of all atoms from a
                        structure file (using parallel processing)
parallel_fit_drc_4p     Fitting four-parameter dose response curves
                        (using parallel processing)
peptide_profile_plot    Peptide abundance profile plot
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
split_metal_name        Convert metal names to search pattern
try_query               Query from URL
ttest_protti            Perform Welch's t-test
viridis_colours         Viridis colour scheme
volcano_plot            Volcano plot
woods_plot              Woods' plot
