Man pages for protti
Bottom-Up Proteomics and LiP-MS Quality Control and Data Analysis Tools

analyse_functional_networkAnalyse protein interaction network for significant hits
anova_prottiPerform ANOVA
assign_missingnessAssignment of missingness types
assign_peptide_typeAssign peptide type
barcode_plotBarcode plot
calculate_aa_scoresCalculate scores for each amino acid position in a protein...
calculate_diff_abundanceCalculate differential abundance between conditions
calculate_go_enrichmentPerform gene ontology enrichment analysis
calculate_imputationSampling of values for imputation
calculate_kegg_enrichmentPerform KEGG pathway enrichment analysis
calculate_protein_abundanceLabel-free protein quantification
calculate_sequence_coverageProtein sequence coverage
calculate_treatment_enrichmentCheck treatment enrichment
create_queueCreates a mass spectrometer queue for Xcalibur
create_structure_contact_mapCreates a contact map of all atoms from a structure file
create_synthetic_dataCreates a synthetic limited proteolysis proteomics dataset
diff_abundanceCalculate differential abundance between conditions
drc_4pDose response curve helper function
drc_4p_plotPlotting of four-parameter dose response curves
extract_metal_bindersExtract metal-bind protein information from UniProt
fetch_alphafold_predictionFetch AlphaFold prediction
fetch_chebiFetch ChEBI database information
fetch_goFetch gene ontology information from geneontology.org
fetch_keggFetch KEGG pathway data from KEGG
fetch_metal_pdbFetch structural information about protein-metal binding from...
fetch_mobidbFetch protein disorder information from MobiDB
fetch_pdbFetch structure information from RCSB
fetch_pdb_structureFetch PDB structure atom data from RCSB
fetch_uniprotFetch protein data from UniProt
fetch_uniprot_proteomeFetch proteome data from UniProt
filter_cvData filtering based on coefficients of variation (CV)
find_all_subsFind all ChEBI sub IDs of an ID
find_chebisFind ChEBI IDs for name patterns
find_peptideFind peptide location
find_peptide_in_structureFinds peptide positions in a PDB structure based on...
fit_drc_4pFitting four-parameter dose response curves
go_enrichmentPerform gene ontology enrichment analysis
imputeImputation of missing values
kegg_enrichmentPerform KEGG pathway enrichment analysis
map_peptides_on_structureMaps peptides onto a PDB structure or AlphaFold prediction
median_normalisationIntensity normalisation
network_analysisAnalyse protein interaction network for significant hits
normaliseIntensity normalisation
parallel_fit_drc_4pFitting four-parameter dose response curves (using parallel...
peptide_profile_plotPeptide abundance profile plot
peptide_typeAssign peptide type
plot_drc_4pPerform gene ontology enrichment analysis
plot_peptide_profilesPeptide abundance profile plot
plot_pval_distributionPlot histogram of p-value distribution
protti_coloursColour scheme for protti
ptsi_pgkStructural analysis example data
pval_distribution_plotPlot histogram of p-value distribution
qc_charge_statesCheck charge state distribution
qc_contaminantsPercentage of contaminants per sample
qc_cvsCheck CV distribution
qc_data_completenessData completeness
qc_idsCheck number of precursor, peptide or protein IDs
qc_intensity_distributionCheck intensity distribution per sample and overall
qc_median_intensitiesMedian run intensities
qc_missed_cleavagesCheck missed cleavages
qc_pcaPlot principal component analysis
qc_peak_widthPeak width over retention time
qc_peptide_typeCheck peptide type percentage share
qc_proteome_coverageProteome coverage per sample and total
qc_sample_correlationCorrelation based hirachical clustering of samples
qc_sequence_coverageProtein coverage distribution
randomise_queueRandomise samples in MS queue
rapamycin_10uMRapamycin 10 uM example data
rapamycin_dose_responseRapamycin dose response example data
read_prottiRead, clean and convert
replace_identified_by_xReplace identified positions in protein sequence by "x"
scale_prottiScaling a vector
sequence_coverageProtein sequence coverage
split_metal_nameConvert metal names to search pattern
treatment_enrichmentCheck treatment enrichment
try_queryQuery from URL
ttest_prottiPerform Welch's t-test
volcano_plotVolcano plot
volcano_prottiVolcano plot
woods_plotWoods' plot
protti documentation built on Sept. 17, 2021, 5:12 p.m.