Files in proBatch

Tools for Diagnostics and Corrections of Batch Effects in Proteomics

README.md

NEWS

NAMESPACE

DESCRIPTION

build/vignette.rds

data/example_proteome.rda

data/example_proteome_matrix.rda

data/example_sample_annotation.rda

data/example_peptide_annotation.rda

R/utility_funcs.R R/correlation-based_diagnostics.R R/initial_assessment.R R/transform_raw.R R/auxiliary.R R/fit_non_linear.R R/normalize.R R/colors_for_annotation.R R/handle_missing_values.R R/proBatch.R R/date_conversion.R R/proteome_wide_diagnostics.R R/plot_split_violinplot.R R/feature_level_diagnostics.R R/data.R R/CV_calculation.R R/correct_batch_effects.R

vignettes/pvca_quantile_normalized.png

vignettes/Batch_effects_workflow_staircase.png

vignettes/proBatch.Rmd man/normalize.Rd man/plot_sample_corr_heatmap.Rd man/fit_nonlinear.Rd man/proBatch.Rd man/color_list_to_df.Rd man/generate_colors_for_numeric.Rd man/create_peptide_annotation.Rd man/define_sample_order.Rd man/matrix_to_long.Rd man/plot_heatmap_generic.Rd man/plot_sample_mean_or_boxplot.Rd man/plot_PVCA.Rd man/dates_to_posix.Rd man/prepare_PVCA_df.Rd man/plot_peptide_corr_distribution.Rd man/example_sample_annotation.Rd man/plot_heatmap_diagnostic.Rd man/example_peptide_annotation.Rd man/plot_CV_distr.df.Rd man/plot_PCA.Rd man/transform_raw_data.Rd man/plot_PVCA.df.Rd man/calculate_sample_corr_distr.Rd man/example_proteome.Rd man/plot_split_violin_with_boxplot.Rd man/calculate_feature_CV.Rd man/sample_annotation_to_colors.Rd man/long_to_matrix.Rd man/correct_batch_effects.Rd man/plot_sample_corr_distribution.Rd man/feature_level_diagnostics.Rd man/plot_CV_distr.Rd man/plot_hierarchical_clustering.Rd man/date_to_sample_order.Rd man/calculate_peptide_corr_distr.Rd man/plot_corr_matrix.Rd man/example_proteome_matrix.Rd man/check_sample_consistency.Rd man/merge_rare_levels.Rd man/plot_protein_corrplot.Rd man/calculate_PVCA.Rd tests/testthat.R tests/spelling.R tests/testthat/test-normalize.R tests/testthat/test-correct_batch_effect.R tests/testthat/test-proteome_wide_diagnostics.R tests/testthat/test-auxiliary.R tests/testthat/test-transform_raw.R tests/testthat/test-initial_assessment.R tests/testthat/test-utility_funcs.R tests/testthat/test-fit_non_linear.R tests/testthat/test-date_conversion.R tests/testthat/test-correlation_based_diagnostics.R tests/testthat/test-colors_for_annotation.R tests/testthat/test-feature_level_diagnostics.R

inst/CITATION

inst/WORDLIST

inst/doc/proBatch.R inst/doc/proBatch.pdf inst/doc/proBatch.Rmd

proBatch documentation built on Nov. 8, 2020, 4:55 p.m.