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_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 |
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 |