Files in protti
Bottom-Up Proteomics and LiP-MS Quality Control and Data Analysis Tools
MD5
NEWS.md
README.md
NAMESPACE
DESCRIPTION
LICENSE
R/calculate_treatment_enrichment.R
R/qc_charge_states.R
R/fetch_mobidb.R
R/qc_missed_cleavages.R
R/qc_proteome_coverage.R
R/replace_identified_by_x.R
R/fetch_metal_pdb.R
R/filter_cv.R
R/ttest_protti.R
R/split_metal_name.R
R/calculate_imputation.R
R/assign_peptide_type.R
R/calculate_diff_abundance.R
R/fetch_alphafold_prediction.R
R/calculate_kegg_enrichment.R
R/map_peptides_on_structure.R
R/qc_ranked_intensities.R
R/randomise_queue.R
R/find_peptide_in_structure.R
R/qc_pca.R
R/fetch_kegg.R
R/fetch_uniprot.R
R/fetch_chebi.R
R/qc_data_completeness.R
R/fetch_alphafold_aligned_error.R
R/data.R
R/parallel_create_structure_contact_map.R
R/assign_missingness.R
R/create_synthetic_data.R
R/create_queue.R
R/barcode_plot.R
R/qc_sequence_coverage.R
R/drc_4p_plot.R
R/qc_ids.R
R/qc_peptide_type.R
R/fetch_go.R
R/find_chebis.R
R/normalise.R
R/create_structure_contact_map.R
R/calculate_protein_abundance.R
R/anova_protti.R
R/drc_4p.R
R/qc_sample_correlation.R
R/woods_plot.R
R/qc_median_intensities.R
R/fetch_pdb_structure.R
R/fetch_pdb.R
R/fetch_quickgo.R
R/calculate_aa_scores.R
R/try_query.R
R/fetch_eco.R
R/find_all_subs.R
R/impute.R
R/find_peptide.R
R/peptide_profile_plot.R
R/extract_metal_binders.R
R/parallel_fit_drc_4p.R
R/zzz.R
R/scale_protti.R
R/read_protti.R
R/volcano_plot.R
R/qc_contaminants.R
R/fetch_uniprot_proteome.R
R/qc_intensity_distribution.R
R/predict_alphafold_domain.R
R/calculate_go_enrichment.R
R/pval_distribution_plot.R
R/qc_peak_width.R
R/calculate_sequence_coverage.R
R/fit_drc_4p.R
R/qc_cvs.R
R/analyse_functional_network.R
inst/CITATION
inst/doc/data_analysis_dose_response_workflow.html
inst/doc/protein_structure_workflow.Rmd
inst/doc/protein_structure_workflow.R
inst/doc/quality_control_workflow.html
inst/doc/data_analysis_single_dose_treatment_workflow.Rmd
inst/doc/data_analysis_dose_response_workflow.Rmd
inst/doc/data_analysis_dose_response_workflow.R
inst/doc/protein_structure_workflow.html
inst/doc/input_preparation_workflow.Rmd
inst/doc/quality_control_workflow.Rmd
inst/doc/input_preparation_workflow.R
inst/doc/quality_control_workflow.R
inst/doc/data_analysis_single_dose_treatment_workflow.R
inst/doc/data_analysis_single_dose_treatment_workflow.html
inst/doc/input_preparation_workflow.html
build/vignette.rds
tests/testthat.R
tests/testthat/test_import.csv
tests/testthat/test-qc_functions.R
tests/testthat/test-fetch_extract_and_enrichment_functions.R
tests/testthat/test-queue_functions.R
tests/testthat/test-auxiliary_functions.R
tests/testthat/test-workflow.R
tests/testthat/test-structure_functions.R
vignettes/protein_structure_workflow.Rmd
vignettes/data_analysis_single_dose_treatment_workflow.Rmd
vignettes/data_analysis_dose_response_workflow.Rmd
vignettes/input_preparation_workflow.Rmd
vignettes/quality_control_workflow.Rmd
vignettes/figures/peptide_map_2hwg_score.png
vignettes/figures/peptide_map_1zmr_score.png
vignettes/figures/peptide_map_2hwg.png
vignettes/figures/interaction_2hwg.png
vignettes/figures/peptide_map_1zmr.png
data/metal_chebi_uniprot.rda
data/metal_list.rda
data/ptsi_pgk.rda
data/rapamycin_dose_response.rda
data/protti_colours.rda
data/rapamycin_10uM.rda
data/metal_go_slim_subset.rda
data/viridis_colours.rda
man/normalise.Rd
man/map_peptides_on_structure.Rd
man/fetch_uniprot.Rd
man/peptide_profile_plot.Rd
man/qc_sequence_coverage.Rd
man/qc_peak_width.Rd
man/calculate_kegg_enrichment.Rd
man/find_peptide.Rd
man/create_structure_contact_map.Rd
man/find_peptide_in_structure.Rd
man/fetch_pdb.Rd
man/qc_contaminants.Rd
man/filter_cv.Rd
man/peptide_type.Rd
man/woods_plot.Rd
man/qc_charge_states.Rd
man/barcode_plot.Rd
man/extract_metal_binders.Rd
man/fetch_metal_pdb.Rd
man/fetch_go.Rd
man/qc_sample_correlation.Rd
man/qc_proteome_coverage.Rd
man/viridis_colours.Rd
man/diff_abundance.Rd
man/parallel_fit_drc_4p.Rd
man/drc_4p_plot.Rd
man/rapamycin_10uM.Rd
man/volcano_protti.Rd
man/fetch_uniprot_proteome.Rd
man/predict_alphafold_domain.Rd
man/parallel_create_structure_contact_map.Rd
man/qc_intensity_distribution.Rd
man/plot_pval_distribution.Rd
man/find_chebis.Rd
man/replace_identified_by_x.Rd
man/calculate_treatment_enrichment.Rd
man/qc_missed_cleavages.Rd
man/volcano_plot.Rd
man/sequence_coverage.Rd
man/fetch_eco.Rd
man/randomise_queue.Rd
man/assign_peptide_type.Rd
man/create_synthetic_data.Rd
man/assign_missingness.Rd
man/fetch_alphafold_prediction.Rd
man/impute.Rd
man/metal_chebi_uniprot.Rd
man/fetch_alphafold_aligned_error.Rd
man/anova_protti.Rd
man/calculate_sequence_coverage.Rd
man/calculate_diff_abundance.Rd
man/try_query.Rd
man/plot_peptide_profiles.Rd
man/read_protti.Rd
man/qc_median_intensities.Rd
man/ttest_protti.Rd
man/qc_cvs.Rd
man/plot_drc_4p.Rd
man/fit_drc_4p.Rd
man/protti_colours.Rd
man/go_enrichment.Rd
man/calculate_aa_scores.Rd
man/analyse_functional_network.Rd
man/ptsi_pgk.Rd
man/drc_4p.Rd
man/find_all_subs.Rd
man/create_queue.Rd
man/qc_peptide_type.Rd
man/calculate_go_enrichment.Rd
man/split_metal_name.Rd
man/scale_protti.Rd
man/calculate_protein_abundance.Rd
man/qc_ranked_intensities.Rd
man/metal_list.Rd
man/qc_pca.Rd
man/fetch_chebi.Rd
man/qc_data_completeness.Rd
man/fetch_mobidb.Rd
man/median_normalisation.Rd
man/fetch_kegg.Rd
man/pval_distribution_plot.Rd
man/rapamycin_dose_response.Rd
man/fetch_pdb_structure.Rd
man/metal_go_slim_subset.Rd
man/fetch_quickgo.Rd
man/kegg_enrichment.Rd
man/network_analysis.Rd
man/treatment_enrichment.Rd
man/qc_ids.Rd
man/calculate_imputation.Rd
man/figures/lifecycle-stable.svg
man/figures/lifecycle-superseded.svg
man/figures/logo.png
man/figures/README-volcano-1.png
man/figures/lifecycle-questioning.svg
man/figures/lifecycle-archived.svg
man/figures/lifecycle-defunct.svg
man/figures/lifecycle-experimental.svg
man/figures/lifecycle-deprecated.svg
man/figures/lifecycle-maturing.svg
