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protti  

Bottom-Up Proteomics and LiP-MS Quality Control and Data Analysis Tools
View on CRAN: Click here


Download and install protti package within the R console
Install from CRAN:
install.packages("protti")

Install from Github:
library("remotes")
install_github("cran/protti")

Install by package version:
library("remotes")
install_version("protti", "0.9.1")



Attach the package and use:
library("protti")
Maintained by
Jan-Philipp Quast
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2021-04-23
Latest Update: 2024-02-17
Description:
Useful functions and workflows for proteomics quality control and data analysis of both limited proteolysis-coupled mass spectrometry (LiP-MS) (Feng et. al. (2014) ) and regular bottom-up proteomics experiments. Data generated with search tools such as 'Spectronaut', 'MaxQuant' and 'Proteome Discover' can be easily used due to flexibility of functions.
How to cite:
Jan-Philipp Quast (2021). protti: Bottom-Up Proteomics and LiP-MS Quality Control and Data Analysis Tools. R package version 0.9.1, https://cran.r-project.org/web/packages/protti. Accessed 03 Dec. 2024.
Previous versions and publish date:
0.1.0 (2021-04-23 10:00), 0.1.1 (2021-05-10 15:10), 0.2.0 (2021-09-17 14:20), 0.2.1 (2022-01-11 18:12), 0.2.2 (2022-03-08 17:40), 0.3.0 (2022-04-12 14:00), 0.3.1 (2022-07-01 10:00), 0.4.0 (2022-09-08 13:00), 0.5.0 (2022-09-29 21:40), 0.6.0 (2023-01-20 11:30), 0.7.0 (2024-02-17 13:20), 0.8.0 (2024-03-28 14:10), 0.9.0 (2024-07-15 20:50)
Other packages that cited protti R package
View protti citation profile
Other R packages that protti depends, imports, suggests or enhances
Complete documentation for protti
Functions, R codes and Examples using the protti R package
Some associated functions: analyse_functional_network . anova_protti . assign_missingness . assign_peptide_type . barcode_plot . calculate_aa_scores . calculate_diff_abundance . calculate_go_enrichment . calculate_imputation . calculate_kegg_enrichment . calculate_protein_abundance . calculate_sequence_coverage . calculate_treatment_enrichment . create_queue . create_structure_contact_map . create_synthetic_data . diff_abundance . drc_4p . drc_4p_plot . extract_metal_binders . fetch_alphafold_aligned_error . fetch_alphafold_prediction . fetch_chebi . fetch_eco . fetch_go . fetch_kegg . fetch_metal_pdb . fetch_mobidb . fetch_pdb . fetch_pdb_structure . fetch_quickgo . fetch_uniprot . fetch_uniprot_proteome . filter_cv . find_all_subs . find_chebis . find_peptide . find_peptide_in_structure . fit_drc_4p . go_enrichment . impute . kegg_enrichment . map_peptides_on_structure . median_normalisation . metal_chebi_uniprot . metal_go_slim_subset . metal_list . network_analysis . normalise . parallel_create_structure_contact_map . parallel_fit_drc_4p . peptide_profile_plot . peptide_type . plot_drc_4p . plot_peptide_profiles . plot_pval_distribution . predict_alphafold_domain . protti_colours . ptsi_pgk . pval_distribution_plot . qc_charge_states . qc_contaminants . qc_cvs . qc_data_completeness . qc_ids . qc_intensity_distribution . qc_median_intensities . qc_missed_cleavages . qc_pca . qc_peak_width . qc_peptide_type . qc_proteome_coverage . qc_ranked_intensities . qc_sample_correlation . qc_sequence_coverage . randomise_queue . rapamycin_10uM . rapamycin_dose_response . read_protti . replace_identified_by_x . scale_protti . sequence_coverage . split_metal_name . treatment_enrichment . try_query . ttest_protti . viridis_colours . volcano_plot . volcano_protti . woods_plot . 
Some associated R codes: analyse_functional_network.R . anova_protti.R . assign_missingness.R . assign_peptide_type.R . barcode_plot.R . calculate_aa_scores.R . calculate_diff_abundance.R . calculate_go_enrichment.R . calculate_imputation.R . calculate_kegg_enrichment.R . calculate_protein_abundance.R . calculate_sequence_coverage.R . calculate_treatment_enrichment.R . create_queue.R . create_structure_contact_map.R . create_synthetic_data.R . data.R . drc_4p.R . drc_4p_plot.R . extract_metal_binders.R . fetch_alphafold_aligned_error.R . fetch_alphafold_prediction.R . fetch_chebi.R . fetch_eco.R . fetch_go.R . fetch_kegg.R . fetch_metal_pdb.R . fetch_mobidb.R . fetch_pdb.R . fetch_pdb_structure.R . fetch_quickgo.R . fetch_uniprot.R . fetch_uniprot_proteome.R . filter_cv.R . find_all_subs.R . find_chebis.R . find_peptide.R . find_peptide_in_structure.R . fit_drc_4p.R . impute.R . map_peptides_on_structure.R . normalise.R . parallel_create_structure_contact_map.R . parallel_fit_drc_4p.R . peptide_profile_plot.R . predict_alphafold_domain.R . pval_distribution_plot.R . qc_charge_states.R . qc_contaminants.R . qc_cvs.R . qc_data_completeness.R . qc_ids.R . qc_intensity_distribution.R . qc_median_intensities.R . qc_missed_cleavages.R . qc_pca.R . qc_peak_width.R . qc_peptide_type.R . qc_proteome_coverage.R . qc_ranked_intensities.R . qc_sample_correlation.R . qc_sequence_coverage.R . randomise_queue.R . read_protti.R . replace_identified_by_x.R . scale_protti.R . split_metal_name.R . try_query.R . ttest_protti.R . volcano_plot.R . woods_plot.R . zzz.R .  Full protti package functions and examples
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