Files in MassDynamics/lfq_processing

Processes Proteomics Files for Quantification.

R/clean_up.R R/condition_name_converter.R R/condition_name_parsing.R R/data.R R/detect_exp_type.R R/get_protein_viz.R R/id_link_table.R R/id_parser.R R/impute_lfq.R R/lfq_transformer.R R/limma_stats_fun.R R/phospho_enrichment_table.R R/protein_quant_runner.R R/qc_report_names_mapping.R R/quantitative_analysis.R R/read_mq_table.R R/tmt_transformer.R R/write_output.R R/zzz.R README.md docs/Quick guide.Rmd inst/install_dependencies.r inst/rmd/QC_CV_modified_peptides.Rmd inst/rmd/QC_CV_peptides.Rmd inst/rmd/QC_CV_proteins.Rmd inst/rmd/QC_PCA_DE_modified_peptides.Rmd inst/rmd/QC_PCA_DE_peptides.Rmd inst/rmd/QC_PCA_DE_proteins.Rmd inst/rmd/QC_PCA_modified_peptides.Rmd inst/rmd/QC_PCA_peptides.Rmd inst/rmd/QC_PCA_proteins.Rmd inst/rmd/QC_PCA_screeplot_modified_peptides.Rmd inst/rmd/QC_PCA_screeplot_peptides.Rmd inst/rmd/QC_PCA_screeplot_proteins.Rmd inst/rmd/QC_Report.Rmd inst/rmd/QC_Report_protein_only.Rmd inst/rmd/QC_TMT_CV_proteins.Rmd inst/rmd/QC_TMT_PCA_DE_proteins.Rmd inst/rmd/QC_TMT_PCA_proteins.Rmd inst/rmd/QC_TMT_PCA_screeplot_proteins.Rmd inst/rmd/QC_TMT_identifications_proteins.Rmd inst/rmd/QC_TMT_imputed_proteins.Rmd inst/rmd/QC_TMT_intensities_boxplots_proteins.Rmd inst/rmd/QC_TMT_intensities_normalised_boxplots_proteins.Rmd inst/rmd/QC_TMT_missed_cleavages_evidence.Rmd inst/rmd/QC_TMT_missing_by_proteins.Rmd inst/rmd/QC_TMT_missing_by_samples_proteins.Rmd inst/rmd/QC_TMT_parent_ion_frac_evidence.Rmd inst/rmd/QC_identifications_PSMs.Rmd inst/rmd/QC_identifications_modified_peptides.Rmd inst/rmd/QC_identifications_modified_peptides_evidence.Rmd inst/rmd/QC_identifications_peptides.Rmd inst/rmd/QC_identifications_peptides_evidence.Rmd inst/rmd/QC_identifications_proteins.Rmd inst/rmd/QC_identifications_proteins_evidence.Rmd inst/rmd/QC_missed_cleavages_evidence.Rmd inst/rmd/QC_missing_by_modified_peptides.Rmd inst/rmd/QC_missing_by_peptides.Rmd inst/rmd/QC_missing_by_proteins.Rmd inst/rmd/QC_missing_by_samples_modified_peptides.Rmd inst/rmd/QC_missing_by_samples_peptides.Rmd inst/rmd/QC_missing_by_samples_proteins.Rmd inst/rmd/QC_samples_correlations_DE_modified_peptides.Rmd inst/rmd/QC_samples_correlations_DE_peptides.Rmd inst/rmd/QC_samples_correlations_DE_proteins.Rmd inst/rmd/QC_samples_correlations_modified_peptides.Rmd inst/rmd/QC_samples_correlations_peptides.Rmd inst/rmd/QC_samples_correlations_proteins.Rmd inst/rmd/QC_samples_correlations_scatter_modified_peptides.Rmd inst/rmd/QC_samples_correlations_scatter_peptides.Rmd inst/rmd/QC_samples_correlations_scatter_proteins.Rmd inst/rmd/tmt_qc_report.Rmd install.R man/assembleComparisonConditionMapping.Rd man/decodeComparisonConditionMapping.Rd man/des_tmt_PXD019880.Rd man/detect_exp_type.Rd man/example_lfq_her2_targetted_therapy_tables.Rd man/getDownCondition.Rd man/getOriginalFromSafe.Rd man/getUpCondition.Rd man/get_names_qc_lfq_all.Rd man/get_names_qc_lfq_protein_only.Rd man/get_names_qc_tmt_protein_only.Rd man/get_protein_viz.Rd man/impute_lfq.Rd man/lfq_quant_analysis.Rd man/lfq_transformer.Rd man/limma_stats_fun.Rd man/oneProteinReplData.Rd man/phospho_enrichment_quant.Rd man/protein_groups_tmt_PXD019880.Rd man/protein_quant_runner.Rd man/render_separate_qcs.Rd man/tmt_transformer.Rd man/writeReplicateData.Rd man/write_output.Rd renv/activate.R tests/data/PXD026936/preprint.pdf tests/testthat.R tests/testthat/test_acceptance_lfq.R tests/testthat/test_acceptance_lfq_protein_only.R tests/testthat/test_acceptance_tmt.R tests/testthat/test_experiment_design_formatter.R tests/testthat/test_get_lfq_intensity_columns.R tests/testthat/test_get_protein_viz.R tests/testthat/test_get_tmt_intensity_columns.R tests/testthat/test_lfq_protein_groups_formatter.R tests/testthat/test_lfq_remove_some_samples.R tests/testthat/test_lfq_with_fractions.R tests/testthat/test_parse_id_columns.R tests/testthat/test_pattern_matcher.R