All functions |
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Analyse protein interaction network for significant hits |
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Perform ANOVA |
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Assignment of missingness types |
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Assign peptide type |
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Barcode plot |
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Calculate scores for each amino acid position in a protein sequence |
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Calculate differential abundance between conditions |
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Perform gene ontology enrichment analysis |
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Sampling of values for imputation |
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Perform KEGG pathway enrichment analysis |
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Label-free protein quantification |
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Protein sequence coverage |
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Check treatment enrichment |
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Protein abundance correction for LiP-data |
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Creates a mass spectrometer queue for Xcalibur |
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Creates a contact map of all atoms from a structure file |
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Creates a synthetic limited proteolysis proteomics dataset |
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Dose response curve helper function |
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Plotting of four-parameter dose response curves |
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Extract metal-binding protein information from UniProt |
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Fetch AlphaFold aligned error |
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Fetch AlphaFold prediction |
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Fetch ChEBI database information |
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Fetch evidence & conclusion ontology |
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Fetch gene ontology information from geneontology.org |
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Fetch KEGG pathway data from KEGG |
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Fetch structural information about protein-metal binding from MetalPDB |
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Fetch protein disorder and mobility information from MobiDB |
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Fetch structure information from RCSB |
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Fetch PDB structure atom data from RCSB |
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Fetch information from the QuickGO API |
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Fetch protein data from UniProt |
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Fetch proteome data from UniProt |
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Data filtering based on coefficients of variation (CV) |
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Find all sub IDs of an ID in a network |
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Find ChEBI IDs for name patterns |
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Find peptide location |
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Finds peptide positions in a PDB structure based on positional matching |
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Fitting four-parameter dose response curves |
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Imputation of missing values |
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Viridis colour scheme |
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Maps peptides onto a PDB structure or AlphaFold prediction |
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List of metal-related ChEBI IDs in UniProt |
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Molecular function gene ontology metal subset |
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List of metals |
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Intensity normalisation |
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Creates a contact map of all atoms from a structure file (using parallel processing) |
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Fitting four-parameter dose response curves (using parallel processing) |
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Peptide abundance profile plot |
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Predict protein domains of AlphaFold predictions |
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Colour scheme for protti |
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Structural analysis example data |
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Plot histogram of p-value distribution |
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Check charge state distribution |
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Percentage of contaminants per sample |
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Check CV distribution |
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Data completeness |
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Check number of precursor, peptide or protein IDs |
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Check intensity distribution per sample and overall |
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Median run intensities |
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Check missed cleavages |
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Plot principal component analysis |
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Peak width over retention time |
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Check peptide type percentage share |
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Proteome coverage per sample and total |
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Check ranked intensities |
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Correlation based hirachical clustering of samples |
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Protein coverage distribution |
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Randomise samples in MS queue |
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Rapamycin 10 uM example data |
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Rapamycin dose response example data |
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Read, clean and convert |
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Replace identified positions in protein sequence by "x" |
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Scaling a vector |
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Convert metal names to search pattern |
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Query from URL |
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Perform Welch's t-test |
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Viridis colour scheme |
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Volcano plot |
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Woods' plot |