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/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/data.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/calculate_aa_scores.R R/try_query.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/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/doc/data_analysis_dose_response_workflow.html
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/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/data_analysis_single_dose_treatment_workflow.Rmd vignettes/data_analysis_dose_response_workflow.Rmd vignettes/input_preparation_workflow.Rmd vignettes/quality_control_workflow.Rmd
data/ptsi_pgk.rda
data/rapamycin_dose_response.rda
data/protti_colours.rda
data/rapamycin_10uM.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/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/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/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/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_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/kegg_enrichment.Rd man/network_analysis.Rd man/treatment_enrichment.Rd man/qc_ids.Rd man/calculate_imputation.Rd
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man/figures/lifecycle-superseded.svg
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/protti_logo.png
man/figures/lifecycle-maturing.svg
protti documentation built on Sept. 17, 2021, 5:12 p.m.