Files in MassDynamics/MassExpression

MassExpression

LICENSE.md R/createCompleteIntensityExperiment.R R/createSummarizedExperiment.R R/data.R R/imputeLFQ.R R/limmaStatsFun.R R/prepareForFiltering.R R/prepare_enrichment.R R/qc_plotting_functions.R R/qc_report_generation.R R/qc_report_names_mapping.R R/runGenericDiscovery.R R/runLimmaPipeline.R R/sanitize_strings.R R/saveOutput.R R/saveOutputV2.R R/utils.R R/writeProteinViz.R README.Rmd README.md data-raw/create-data-for-testing.R data-raw/create-sample-data.R inst/rmd/QC_CV_proteins.Rmd inst/rmd/QC_CV_table_proteins.Rmd inst/rmd/QC_DE_summary_proteins.Rmd inst/rmd/QC_PCA_DE_proteins.Rmd inst/rmd/QC_PCA_proteins.Rmd inst/rmd/QC_PCA_screeplot_proteins.Rmd inst/rmd/QC_RLE_normalised_proteins.Rmd inst/rmd/QC_RLE_raw_proteins.Rmd inst/rmd/QC_consistent_identifications_proteins.Rmd inst/rmd/QC_identifications_proteins.Rmd inst/rmd/QC_imputed_proteins.Rmd inst/rmd/QC_intensities_boxplots_proteins.Rmd inst/rmd/QC_missing_by_proteins.Rmd inst/rmd/QC_missing_by_samples_proteins.Rmd inst/rmd/QC_missingness_patterns_proteins.Rmd inst/rmd/QC_report.Rmd inst/rmd/QC_samples_correlations_DE_proteins.Rmd inst/rmd/QC_samples_correlations_proteins.Rmd install.R man/MassExpressionTOProtCountV2.Rd man/SEToLongDT.Rd man/computeImputedCounts.Rd man/computeReplicateCounts.Rd man/compute_pcas.Rd man/createCompleteIntensityExperiment.Rd man/createSummarizedExperiment.Rd man/fragpipe_data.Rd man/generate_qc_report.Rd man/generate_separate_qc_reports.Rd man/get_names_qc.Rd man/imputeLFQ.Rd man/initialiseLongIntensityDT.Rd man/limmaStatsFun.Rd man/listComparisonExperiments.Rd man/makeRLEBoxplotInteractive.Rd man/mq_lfq_data.Rd man/normaliseIntensity.Rd man/oneGroupReplDataV2.Rd man/oneProteinReplData.Rd man/pd_iPRG_data.Rd man/plot_chosen_pca_experiment.Rd man/plot_condition_cv_distribution.Rd man/plot_consistent_proteins_by_replicate.Rd man/plot_density_distr.Rd man/plot_imputed_vs_not.Rd man/plot_log_measurement_boxplot.Rd man/plot_ma.Rd man/plot_mds_experiment.Rd man/plot_missingness_heatmap.Rd man/plot_n_identified_proteins_by_replicate.Rd man/plot_pca_experiment.Rd man/plot_protein_missingness.Rd man/plot_replicate_measured_values.Rd man/plot_rle_boxplot.Rd man/plot_samples_correlation_matrix.Rd man/plot_volcano.Rd man/prepareForFiltering.Rd man/preparePlottingData.Rd man/runGenericDiscovery.Rd man/runLimmaPipeline.Rd man/sanitize_strings.Rd man/sanitize_strings_in_dataframe.Rd man/saveOutput.Rd man/select_features_for_pca.Rd man/writeLimmaStatisticsTable.Rd man/writeOutputFile.Rd man/writeProteinQuantIntensities.Rd man/writeProteinViz.Rd man/writeReplicateData.Rd man/writeReplicateDataV2.Rd renv/activate.R tests/testthat.R tests/testthat/test_acceptance_runGenericDiscovery.R tests/testthat/test_condition_name_encoder.R tests/testthat/test_imputeLFQ.R tests/testthat/test_limmaStatsFun.R tests/testthat/test_normaliseIntensity.R tests/testthat/test_sanitize_strings.R tests/testthat/test_writeReplicatesData.R vignettes/vignette.Rmd