Files in wolski/prolfqua
Proteomics Label Free Quantification
.Rbuildignore
.github/CONTRIBUTING.md
.github/ISSUE_TEMPLATE/bug_report.md
.github/ISSUE_TEMPLATE/custom.md
.github/ISSUE_TEMPLATE/feature_request.md
.github/workflows/r.yaml
.gitignore
BinaryFiles
CODE_OF_CONDUCT.md
DESCRIPTION
LICENSE.md
NAMESPACE
R/A_dataset_docu.R
R/AnalysisConfiguration.R
R/AnalysisParameters.R
R/AnalysisTableAnnotation.R
R/Benchmark.R
R/Contrasts.R
R/ContrastsInterface.R
R/ContrastsModerated.R
R/ContrastsPlotter.R
R/ContrastsProDA.R
R/ContrastsROPECA.R
R/ContrastsSimpleImpute.R
R/ContrastsTable.R
R/DEPRECATED.R
R/LFQData.R
R/LFQDataAggregator.R
R/LFQDataPlotter.R
R/LFQDataStats.R
R/LFQDataSummariser.R
R/LFQDataTransformer.R
R/LFQDataWriter.R
R/Model.R
R/ModelInterface.R
R/ProjectStructure.R
R/ProteinAnnotation.R
R/simulate_LFQ_data.R
R/squeezeVarRob.R
R/tidyMS_MQ_workflow.R
R/tidyMS_R6Model.R
R/tidyMS_R6_ConcreteConfigurations.R
R/tidyMS_R6_Modelling.R
R/tidyMS_R6_TransitionCorrelations.R
R/tidyMS_aggregation.R
R/tidyMS_missigness.R
R/tidyMS_missigness_V2.R
R/tidyMS_plotting.R
R/tidyMS_stats.R
R/tidyMS_write.R
R/utilities.R
R/vignetteHelpers.R
README.md
_pkgdown.yml
conda/build.sh
conda/environment-dev.yaml
conda/meta.yaml
data/data_IonstarProtein_subsetNorm.rda
data/data_SAINTe_output.rda
data/data_Yeast2Factor.rda
data/data_basicModel_p1807.rda
data/data_benchmarkExample.rda
data/data_checksummarizationrobust87.rda
data/data_checksummarizerobust.rda
data/data_checksummarizerobust69.rda
data/data_correlatedPeptideList.rda
data/data_factor_levelContrasts.rda
data/data_interactionModel_p1807.rda
data/data_ionstar.rda
data/data_modellingResult_A.rda
data/data_multigroupFC.rda
data/data_skylinePRMSample_A.rda
data/data_skylineSRM_HL_A.rda
data/data_spectronautDIA250_A.rda
data/data_test_confusion_matrix_scores.rda
inst/.gitignore
inst/CITATION
inst/Dockerfile
inst/extdata/metadata.csv
man/AnalysisConfiguration.Rd
man/AnalysisParameters.Rd
man/AnalysisTableAnnotation.Rd
man/Benchmark.Rd
man/Contrasts.Rd
man/ContrastsInterface.Rd
man/ContrastsMissing.Rd
man/ContrastsModerated.Rd
man/ContrastsPlotter.Rd
man/ContrastsProDA.Rd
man/ContrastsROPECA.Rd
man/ContrastsTable.Rd
man/INTERNAL_FUNCTIONS_BY_FAMILY.Rd
man/LFQData.Rd
man/LFQDataAggregator.Rd
man/LFQDataPlotter.Rd
man/LFQDataStats.Rd
man/LFQDataSummariser.Rd
man/LFQDataToSummarizedExperiment.Rd
man/LFQDataTransformer.Rd
man/LFQDataWriter.Rd
man/LR_test.Rd
man/MissingHelpers.Rd
man/Model.Rd
man/ModelInterface.Rd
man/PACKAGE_DATA.Rd
man/ProjectStructure.Rd
man/ProteinAnnotation.Rd
man/R6_extract_values.Rd
man/UpSet_interaction_missing_stats.Rd
man/UpSet_missing_stats.Rd
man/adjust_p_values.Rd
man/aggregate_contrast.Rd
man/aggregate_intensity_topN.Rd
man/apply_to_response_matrix.Rd
man/build_model.Rd
man/complete_cases.Rd
man/concrete_AnalysisConfiguration.Rd
man/contrasts_fisher_exact.Rd
man/contrasts_linfct.Rd
man/cor_jackknife_matrix.Rd
man/cor_order.Rd
man/data_IonstarProtein_subsetNorm.Rd
man/data_SAINTe_output.Rd
man/data_Yeast2Factor.Rd
man/data_basicModel_p1807.Rd
man/data_benchmarkExample.Rd
man/data_checksummarizationrobust87.Rd
man/data_checksummarizerobust.Rd
man/data_checksummarizerobust69.Rd
man/data_correlatedPeptideList.Rd
man/data_factor_levelContrasts.Rd
man/data_interactionModel_p1807.Rd
man/data_ionstar.Rd
man/data_modellingResult_A.Rd
man/data_multigroupFC.Rd
man/data_skylinePRMSample_A.Rd
man/data_skylineSRM_HL_A.Rd
man/data_spectronautDIA250_A.Rd
man/data_test_confusion_matrix_scores.Rd
man/dot-get_robscales.Rd
man/dot-missigness_impute_interactions.Rd
man/dot-summarise_missing_contrasts.Rd
man/estimate_intensity.Rd
man/figures/imgfile.png
man/filter_byQValue.Rd
man/filter_difference.Rd
man/filter_proteins_by_peptide_count.Rd
man/find_package_file.Rd
man/get_UniprotID_from_fasta_header.Rd
man/get_anova_df.Rd
man/get_complete_model_fit.Rd
man/get_contrast.Rd
man/get_imputed_contrasts.Rd
man/get_p_values_pbeta.Rd
man/get_robscales.Rd
man/hierarchy_counts.Rd
man/hierarchy_counts_sample.Rd
man/intensity_summary_by_hkeys.Rd
man/interaction_missing_stats.Rd
man/ionstar_bench_preprocess.Rd
man/isSingular_lm.Rd
man/jackknife.Rd
man/jackknife_matrix.Rd
man/lfq_power_t_test_proteins.Rd
man/lfq_power_t_test_quantiles.Rd
man/lfq_power_t_test_quantiles_V2.Rd
man/lfq_write_table.Rd
man/linfct_all_possible_contrasts.Rd
man/linfct_factors_contrasts.Rd
man/linfct_from_model.Rd
man/linfct_matrix_contrasts.Rd
man/make_benchmark.Rd
man/make_interaction_column.Rd
man/make_reduced_hierarchy_config.Rd
man/matrix_to_tibble.Rd
man/medpolish_estimate.Rd
man/medpolish_estimate_df.Rd
man/medpolish_estimate_dfconfig.Rd
man/medpolish_protein_estimates.Rd
man/merge_contrasts_results.Rd
man/missigness_histogram.Rd
man/missigness_impute_factors_interactions.Rd
man/missingness_per_condition.Rd
man/missingness_per_condition_cumsum.Rd
man/model_analyse.Rd
man/model_summary.Rd
man/moderated_p_limma.Rd
man/moderated_p_limma_long.Rd
man/ms_bench_add_scores.Rd
man/ms_bench_auc.Rd
man/multigroup_volcano.Rd
man/my_contest.Rd
man/my_contrast.Rd
man/my_contrast_V1.Rd
man/my_contrast_V2.Rd
man/my_glht.Rd
man/names_to_matrix.Rd
man/normalize_log2_robscale.Rd
man/nr_B_in_A.Rd
man/nr_B_in_A_per_sample.Rd
man/nr_obs_experiment.Rd
man/nr_obs_sample.Rd
man/old2new.Rd
man/pairs_smooth.Rd
man/pairs_w_abline.Rd
man/panel_cor.Rd
man/panel_hist.Rd
man/pivot_model_contrasts_2_Wide.Rd
man/plot_NA_heatmap.Rd
man/plot_estimate.Rd
man/plot_heatmap.Rd
man/plot_heatmap_cor.Rd
man/plot_hierarchies_add_quantline.Rd
man/plot_hierarchies_boxplot.Rd
man/plot_hierarchies_boxplot_df.Rd
man/plot_hierarchies_line.Rd
man/plot_hierarchies_line_df.Rd
man/plot_intensity_distribution_violin.Rd
man/plot_lmer_model_and_data.Rd
man/plot_lmer_peptide_noRandom.Rd
man/plot_lmer_peptide_predictions.Rd
man/plot_lmer_predicted_interactions.Rd
man/plot_pca.Rd
man/plot_raster.Rd
man/plot_sample_correlation.Rd
man/plot_screeplot.Rd
man/plot_stat_density.Rd
man/plot_stat_density_median.Rd
man/plot_stat_violin.Rd
man/plot_stat_violin_median.Rd
man/plot_stdv_vs_mean.Rd
man/pooled_var.Rd
man/prolfqua_data.Rd
man/rank_by_NA.Rd
man/rank_peptide_by_intensity.Rd
man/remove_NA_rows.Rd
man/remove_large_QValues.Rd
man/remove_small_intensities.Rd
man/render_MQSummary_rmd.Rd
man/response_as_matrix.Rd
man/response_matrix_as_tibble.Rd
man/rlm_estimate.Rd
man/rlm_estimate_dfconfig.Rd
man/robust_scale.Rd
man/sample_subset.Rd
man/scale_with_subset.Rd
man/scale_with_subset_by_factors.Rd
man/scriptCopyHelperVec.Rd
man/separate_factors.Rd
man/separate_hierarchy.Rd
man/setup_analysis.Rd
man/sim_lfq_data.Rd
man/sim_lfq_data_peptide_config.Rd
man/sim_lfq_data_protein_2Factor_config.Rd
man/sim_lfq_data_protein_config.Rd
man/spread_response_by_IsotopeLabel.Rd
man/squeezeVarRob.Rd
man/strategy.Rd
man/summarise_QValues.Rd
man/summarize_hierarchy.Rd
man/summarize_stats.Rd
man/summarize_stats_factors.Rd
man/summary_ROPECA_median_p.scaled.Rd
man/table_facade.Rd
man/table_factors.Rd
man/tidy_to_wide.Rd
man/tidy_to_wide_config.Rd
man/transform_work_intensity.Rd
man/volcano_Plotly.Rd
man/which_missing.Rd
prolfqua.Rproj
tests/testthat.R
tests/testthat/.gitignore
tests/testthat/cleanup.R
tests/testthat/test-plotting_functions.R
tests/testthat/test-tidyconfig_functions.R
vignettes/.gitignore
vignettes/.install_extras
vignettes/Comparing2Groups.Rmd
vignettes/CreatingConfigurations.Rmd
vignettes/Modelling2Factors.Rmd
vignettes/QCandSampleSize.Rmd
vignettes/QualityControlAndSampleSizeEstimation.Rmd
vignettes/SimulateData.Rmd
vignettes/TestingMissingInference.Rmd
vignettes/prolfqua.bib
