General data reading and preparation functions.
tor_read_protein_counts_data()
Read protein counts data
tor_read_svm_data_file()
Read SVM data file
tor_filter_label_rate_fits()
Filter label rate fits
tor_filter_peptides_by_spectral_fit_quality()
Filter peptides
tor_recode_protein_ids()
Rename proteins based on protein mapping file
Functions that add additional information to the dataset.
tor_add_metadata()
Add metadata
tor_add_protein_counts_info()
Add protein counts info
tor_add_uniprot_info()
Add uniprot information
Functions to perform calculations on protein turnover data.
tor_calculate_degradation_dissipation()
Calculate degradation rate
tor_calculate_growth_params()
Calculate growth parameters
tor_calculate_label_rate()
Calculate protein or peptide labeling rate
tor_calculate_labeled_fraction()
Calculate labeled fraction
Functions to visualize the data.
tor_plot_label_rate_error()
Plot label rate error
tor_plot_label_rate_hist()
Plot label rate histogram
tor_plot_labeling_curves()
Plot labeling curves
Functions to fetch information from protein databases.
tor_fetch_kegg_details()
Fetch KEGG details
tor_fetch_kegg_pathway_details()
Fetch KEGG pathway details
tor_fetch_kegg_pathway_maps()
Fetch KEGG pathway maps
tor_fetch_kegg_pathways_for_species()
Fetch all KEGG pathways for a species
tor_fetch_kegg_species()
Fetch KEGG species
tor_fetch_uniprot_proteins()
Fetch uniprot information
tor_fetch_uniprot_species()
Fetch uniprot species
Miscellaneous utility functions
tor_remove_list_columns()
Remove complex data
tor_show_package_structure()
Generate flow chart