Files in jpquast/protti

Bottom-Up Proteomics and LiP-MS Quality Control and Data Analysis Tools

LICENSE.md NEWS.md R/analyse_functional_network.R R/anova_protti.R R/assign_missingness.R R/assign_peptide_type.R R/barcode_plot.R R/calculate_aa_scores.R R/calculate_diff_abundance.R R/calculate_go_enrichment.R R/calculate_imputation.R R/calculate_kegg_enrichment.R R/calculate_protein_abundance.R R/calculate_sequence_coverage.R R/calculate_treatment_enrichment.R R/correct_lip_for_abundance.R R/create_queue.R R/create_structure_contact_map.R R/create_synthetic_data.R R/data.R R/drc_4p.R R/drc_4p_plot.R R/extract_metal_binders.R R/fetch_alphafold_aligned_error.R R/fetch_alphafold_prediction.R R/fetch_chebi.R R/fetch_eco.R R/fetch_go.R R/fetch_kegg.R R/fetch_metal_pdb.R R/fetch_mobidb.R R/fetch_pdb.R R/fetch_pdb_structure.R R/fetch_quickgo.R R/fetch_uniprot.R R/fetch_uniprot_proteome.R R/filter_cv.R R/find_all_subs.R R/find_chebis.R R/find_peptide.R R/find_peptide_in_structure.R R/fit_drc_4p.R R/impute.R R/map_peptides_on_structure.R R/normalise.R R/parallel_create_structure_contact_map.R R/parallel_fit_drc_4p.R R/peptide_profile_plot.R R/predict_alphafold_domain.R R/pval_distribution_plot.R R/qc_charge_states.R R/qc_contaminants.R R/qc_cvs.R R/qc_data_completeness.R R/qc_ids.R R/qc_intensity_distribution.R R/qc_median_intensities.R R/qc_missed_cleavages.R R/qc_pca.R R/qc_peak_width.R R/qc_peptide_type.R R/qc_proteome_coverage.R R/qc_ranked_intensities.R R/qc_sample_correlation.R R/qc_sequence_coverage.R R/randomise_queue.R R/read_protti.R R/replace_identified_by_x.R R/scale_protti.R R/split_metal_name.R R/try_query.R R/ttest_protti.R R/volcano_plot.R R/woods_plot.R R/zzz.R README.Rmd README.md cran-comments.md data-raw/metal_chebi_uniprot.R data-raw/metal_go_slim_subset.R data-raw/metal_list.R data-raw/protti_colours.R data-raw/ptsi_pgk.R data-raw/rapamycin_10uM.R data-raw/rapamycin_dose_response.R data-raw/viridis_colours.R man/analyse_functional_network.Rd man/anova_protti.Rd man/assign_missingness.Rd man/assign_peptide_type.Rd man/barcode_plot.Rd man/calculate_aa_scores.Rd man/calculate_diff_abundance.Rd man/calculate_go_enrichment.Rd man/calculate_imputation.Rd man/calculate_kegg_enrichment.Rd man/calculate_protein_abundance.Rd man/calculate_sequence_coverage.Rd man/calculate_treatment_enrichment.Rd man/correct_lip_for_abundance.Rd man/create_queue.Rd man/create_structure_contact_map.Rd man/create_synthetic_data.Rd man/diff_abundance.Rd man/drc_4p.Rd man/drc_4p_plot.Rd man/extract_metal_binders.Rd man/fetch_alphafold_aligned_error.Rd man/fetch_alphafold_prediction.Rd man/fetch_chebi.Rd man/fetch_eco.Rd man/fetch_go.Rd man/fetch_kegg.Rd man/fetch_metal_pdb.Rd man/fetch_mobidb.Rd man/fetch_pdb.Rd man/fetch_pdb_structure.Rd man/fetch_quickgo.Rd man/fetch_uniprot.Rd man/fetch_uniprot_proteome.Rd man/filter_cv.Rd man/find_all_subs.Rd man/find_chebis.Rd man/find_peptide.Rd man/find_peptide_in_structure.Rd man/fit_drc_4p.Rd man/go_enrichment.Rd man/impute.Rd man/kegg_enrichment.Rd man/mako_colours.Rd man/map_peptides_on_structure.Rd man/median_normalisation.Rd man/metal_chebi_uniprot.Rd man/metal_go_slim_subset.Rd man/metal_list.Rd man/network_analysis.Rd man/normalise.Rd man/parallel_create_structure_contact_map.Rd man/parallel_fit_drc_4p.Rd man/peptide_profile_plot.Rd man/peptide_type.Rd man/plot_drc_4p.Rd man/plot_peptide_profiles.Rd man/plot_pval_distribution.Rd man/predict_alphafold_domain.Rd man/protti_colours.Rd man/ptsi_pgk.Rd man/pval_distribution_plot.Rd man/qc_charge_states.Rd man/qc_contaminants.Rd man/qc_cvs.Rd man/qc_data_completeness.Rd man/qc_ids.Rd man/qc_intensity_distribution.Rd man/qc_median_intensities.Rd man/qc_missed_cleavages.Rd man/qc_pca.Rd man/qc_peak_width.Rd man/qc_peptide_type.Rd man/qc_proteome_coverage.Rd man/qc_ranked_intensities.Rd man/qc_sample_correlation.Rd man/qc_sequence_coverage.Rd man/randomise_queue.Rd man/rapamycin_10uM.Rd man/rapamycin_dose_response.Rd man/read_protti.Rd man/replace_identified_by_x.Rd man/scale_protti.Rd man/sequence_coverage.Rd man/split_metal_name.Rd man/treatment_enrichment.Rd man/try_query.Rd man/ttest_protti.Rd man/viridis_colours.Rd man/volcano_plot.Rd man/volcano_protti.Rd man/woods_plot.Rd revdep/README.md revdep/cran.md revdep/failures.md revdep/problems.md tests/testthat.R tests/testthat/test-auxiliary_functions.R tests/testthat/test-fetch_extract_and_enrichment_functions.R tests/testthat/test-qc_functions.R tests/testthat/test-queue_functions.R tests/testthat/test-structure_functions.R tests/testthat/test-workflow.R vignettes/data_analysis_dose_response_workflow.Rmd vignettes/data_analysis_single_dose_treatment_workflow.Rmd vignettes/input_preparation_workflow.Rmd vignettes/protein_structure_workflow.Rmd vignettes/quality_control_workflow.Rmd