Files in CambridgeCentreForProteomics/camprotR

Processing, analysing and visualising CCP proteomics data

R/append_fasta.R R/camprotR-package.R R/combine_runs.R R/count_features_per_protein.R R/dep_gene2cat.R R/dep_results.R R/download_ccp_crap.R R/estimate_incorporation.R R/filter_TMT_PSMs.R R/get_cat_palette.R R/get_ratio.R R/go.R R/lfq_oops_rnase.R R/make_fasta.R R/modifications.R R/normalise.R R/parse_features.R R/pep_oops_1.R R/pep_oops_2.R R/pep_oops_3.R R/pep_oops_4.R R/pep_silac_p0.R R/pep_silac_p4.R R/psm_oops_1.R R/psm_oops_2.R R/psm_oops_3.R R/psm_oops_4.R R/psm_silac_p4.R R/psm_tmt_phospho.R R/psm_tmt_total.R R/ptm.R R/qc_plots.R R/restrict_features_per_protein.R R/silac.R R/silac_psm_seq_int.R R/theme_camprot.R R/theme_csd.R R/tmt_qc_plots.R R/utilities.R README.Rmd README.md data-raw/dep_gene2cat.R data-raw/dep_results.R data-raw/lfq_oops_rnase.R data-raw/pep_silac_p0.R data-raw/pep_silac_p4.R data-raw/psm_silac_p4.R data-raw/psm_tmt_phospho.R data-raw/psm_tmt_total.R data-raw/silac_comparison.R data-raw/silac_p4.R man/add_PTM_positions.Rd man/add_peptide_positions.Rd man/add_site_sequence.Rd man/append_fasta.Rd man/camprotR-package.Rd man/center_normalise_to_ref.Rd man/check_uniprot_release.Rd man/compare_IDs.Rd man/compare_sequences_per_protein.Rd man/compare_single_master.Rd man/count_features_per_protein.Rd man/dep_gene2cat.Rd man/dep_results.Rd man/determine_ancestor_function.Rd man/determine_offspring_function.Rd man/download_ccp_crap.Rd man/estimate_go_overrep.Rd man/estimate_incorporation.Rd man/expand_terms.Rd man/filter_TMT_PSMs.Rd man/get_all_mappings.Rd man/get_ancestor_go.Rd man/get_cat_palette.Rd man/get_ccp_crap.Rd man/get_enriched_go.Rd man/get_incorporation.Rd man/get_medians.Rd man/get_notch_per_protein.Rd man/get_parsimony_pep2prot.Rd man/get_psm_metrics.Rd man/get_psm_silac_mod_regex.Rd man/get_ratio.Rd man/get_sequence.Rd man/get_sequence2protein.Rd man/lfq_oops_rnase_pep.Rd man/lfq_oops_rnase_psm.Rd man/make_fasta.Rd man/match_proteins.Rd man/parse_PTM_scores.Rd man/parse_features.Rd man/pep_oops_1.Rd man/pep_oops_2.Rd man/pep_oops_3.Rd man/pep_oops_4.Rd man/pep_silac_p0.Rd man/pep_silac_p4.Rd man/plot_TMT_notch.Rd man/plot_below_notch_per_prot.Rd man/plot_fraction_below_notch_per_prot.Rd man/plot_go.Rd man/plot_incorporation.Rd man/plot_missing_SN.Rd man/plot_missing_SN_per_sample.Rd man/plot_quant.Rd man/psm_oops_1.Rd man/psm_oops_2.Rd man/psm_oops_3.Rd man/psm_oops_4.Rd man/psm_silac_p4.Rd man/psm_tmt_phospho.Rd man/psm_tmt_total.Rd man/psm_to_peptide_style_modifications.Rd man/read_infiles.Rd man/remove_dots.Rd man/remove_redundant_go.Rd man/remove_silac_modifications.Rd man/remove_x.Rd man/restrict_features_per_protein.Rd man/silac_psm_seq_int.Rd man/sub_crap.Rd man/theme_camprot.Rd man/theme_csd.Rd man/update_average_sn.Rd tests/testthat.R tests/testthat/_snaps/go.md tests/testthat/setup.R tests/testthat/test-append_fasta.R tests/testthat/test-combine_runs.R tests/testthat/test-count_features_per_protein.R tests/testthat/test-download_ccp_crap.R tests/testthat/test-estimate_incorporation.R tests/testthat/test-filter_TMT_PSMs.R tests/testthat/test-get_cat_palette.R tests/testthat/test-get_ratio.R tests/testthat/test-go.R tests/testthat/test-modifications.R tests/testthat/test-normalise.R tests/testthat/test-parse_features.R tests/testthat/test-ptm.R tests/testthat/test-qc_plots.R tests/testthat/test-restrict_features_per_protein.R tests/testthat/test-setup.R tests/testthat/test-silac.R tests/testthat/test-silac_psm_seq_int.R tests/testthat/test-theme_camprot.R tests/testthat/test-tmt_qc_plots.R tests/testthat/test-utilities.R vignettes/LFQ_parse_qc_protein_inference.Rmd vignettes/SILAC.Rmd vignettes/TMT_PSM_QC_Summarisation.Rmd vignettes/crap.Rmd vignettes/msnset.Rmd