Files in HaDeX2

Analysis and Visualisation of Hydrogen/Deuterium Exchange Mass Spectrometry Data

MD5

NEWS.md README.md

NAMESPACE

DESCRIPTION

CHANGELOG

R/create_control_dataset.R R/plot_coverage_heatmap.R R/plot_differential_butterfly.R R/plot_volcano.R R/alpha_dat.R R/HaDeXify.R R/read_hdx.R R/plot_aggregated_uptake.R R/calculate_aggregated_difference.R R/create_aggregated_uptake_dataset.R R/plot_manhattan.R R/create_kinetic_dataset.R R/get_residue_positions.R R/plot_butterfly.R R/plot_chiclet.R R/reconstruct_sequence.R R/update_hdexaminer_file.R R/plot_aggregated_uptake_structure.R R/calculate_p_value.R R/calculate_diff_uptake.R R/calculate_state_uptake.R R/plot_differential_uptake_curve.R R/plot_state_comparison.R R/show_diff_uptake_data.R R/calculate_kinetics.R R/create_p_diff_uptake_dataset_with_confidence.R R/HaDeX-package.R R/calculate_confidence_limit_values.R R/plot_uncertainty.R R/calculate_auc.R R/create_state_uptake_dataset.R R/calculate_aggregated_test_results.R R/overlaps.R R/plot_position_frequency.R R/show_kinetic_data.R R/calculate_peptide_kinetics.R R/create_aggregated_difference_dataset.R R/plot_amino_distribution.R R/plot_uptake_curve.R R/HaDeX_gui.R R/create_diff_uptake_dataset.R R/replicates.R R/show_coverage_heatmap_data.R R/plot_coverage.R R/plot_differential_chiclet.R R/calculate_masses.R R/hdx_data_class.R R/quality_control.R R/plot_aggregated_difference.R R/show_data.R R/create_state_comparison_dataset.R R/markdown_texts.R R/zzz.R R/prepare_hdxviewer_export.R R/plot_differential.R R/calculate_aggregated_uptake.R R/getters.R R/plot_replicate_mass_uptake.R R/create_uptake_dataset.R R/calculate_back_exchange.R R/add_stat_dependency.R R/name_getters.R R/create_p_diff_uptake_dataset.R R/utils.R

inst/db_eEF1Ba.png

inst/CITATION

inst/WORDLIST

inst/doc/transformation.Rmd inst/doc/glossary.Rmd inst/doc/datafiles.R

inst/doc/example.html

inst/doc/glossary.R inst/doc/mass_comparison.R inst/doc/example.R inst/doc/visualization.R inst/doc/transformation.R inst/doc/data_input.R

inst/doc/version_comparison.html

inst/doc/statistics.Rmd

inst/doc/visualization.html

inst/doc/usage.html

inst/doc/datafiles.Rmd inst/doc/example.Rmd

inst/doc/data_input.html

inst/doc/statistics.html

inst/doc/data_input.Rmd inst/doc/visualization.Rmd

inst/doc/quality_control.html

inst/doc/usage.Rmd inst/doc/quality_control.Rmd inst/doc/quality_control.R

inst/doc/mass_comparison.html

inst/doc/transformation.html

inst/doc/usage.R

inst/doc/datafiles.html

inst/doc/version_comparison.Rmd inst/doc/mass_comparison.Rmd inst/doc/version_comparison.R inst/doc/statistics.R

inst/doc/glossary.html

inst/HaDeX/www/HaDeX_logo.RDS

inst/HaDeX/data/KD_180110_CD160_HVEM.csv

inst/HaDeX/data/SecA_monomer.pdb

inst/HaDeX/data/alpha.csv

inst/HaDeX/data/SecA_cluster_wt_ADP.csv

inst/HaDeX/data/Model_eEF1Balpha.pdb

build/vignette.rds

build/partial.rdb

tests/testthat.R tests/spelling.R tests/testthat/test-diff_deut_uptake_calculations.R tests/testthat/test-calculate_aggregated_difference.R tests/testthat/test-plot_volcano.R tests/testthat/test-show_replicate_histogram_data.R tests/testthat/test-create_overlap_distribution_dataset.R tests/testthat/test-calculate_back_exchange.R tests/testthat/test-get_protein_coverage.R tests/testthat/test-calculate_p_value.R tests/testthat/test-calculate_aggregated_uptake.R tests/testthat/test-create_aggregated_test_results.R tests/testthat/test-show_uc_data.R tests/testthat/test-show_uptake_data.R tests/testthat/test-reconstruct_sequence.R tests/testthat/test-name_getters.R tests/testthat/test-quality_control.R tests/testthat/test-calculate_exp_mass.R tests/testthat/test-create_p_diff_uptake_dataset.R tests/testthat/test-plot_state_comparison.R tests/testthat/test-calculate_auc.R tests/testthat/test-show_overlap_data.R tests/testthat/test-plot_coverage.R tests/testthat/test-plot_differential_uptake_curve.R tests/testthat/test-create_diff_uptake_dataset.R tests/testthat/test-get_n_replicates.R tests/testthat/test-plot_position_frequency.R tests/testthat/test-deut_uptake_calculations.R tests/testthat/test-plot_peptide_mass_measurement.R tests/testthat/test-plot_manhattan.R tests/testthat/test-plot_replicate_mass_uptake.R tests/testthat/test-create_uptake_dataset.R tests/testthat/test-plot_peptide_charge_measurement.R tests/testthat/test-show_coverage_heatmap_data.R tests/testthat/test-plot_uptake_curve.R tests/testthat/test-get_peptide_sequence.R tests/testthat/test-plot_overlap.R tests/testthat/test-plot_chiclet.R tests/testthat/test-read_hdx.R tests/testthat/test-show_diff_uptake_data.R tests/testthat/test-create_p_diff_uptake_dataset_with_confidence.R tests/testthat/test-plot_differential.R tests/testthat/test-plot_butterfly.R tests/testthat/test-get_protein_redundancy.R tests/testthat/test-plot_differential_butterfly.R tests/testthat/helper-params.R tests/testthat/test-plot_replicate_histogram.R tests/testthat/test-show_peptide_charge_measurement.R tests/testthat/test-prepare_hdxviewer_export.R tests/testthat/test-show_diff_uptake_data_confidence.R tests/testthat/test-calculate_MHP.R tests/testthat/test-create_replicate_dataset.R tests/testthat/test-show_peptide_mass_measurement.R tests/testthat/test-plot_coverage_heatmap.R tests/testthat/test-plot_uncertainty.R tests/testthat/test-plot_differential_chiclet.R

tests/testthat/_snaps/plot_peptide_charge_measurement/peptide-charge-measurement-plot.svg

tests/testthat/_snaps/plot_peptide_mass_measurement/peptide-mass-measurement-plot.svg

tests/testthat/_snaps/plot_state_comparison/state-comparison-plot.svg

tests/testthat/_snaps/plot_state_comparison/theo-state-comparison-plot.svg

tests/testthat/_snaps/plot_state_comparison/theo-frac-state-comparison-plot.svg

tests/testthat/_snaps/plot_state_comparison/frac-state-comparison-plot.svg

tests/testthat/_snaps/plot_uptake_curve/frac-kinetic-plot-bars.svg

tests/testthat/_snaps/plot_uptake_curve/theo-log-kinetic-plot-ribbon.svg

tests/testthat/_snaps/plot_uptake_curve/kinetic-plot-bars-line.svg

tests/testthat/_snaps/plot_uptake_curve/theo-frac-kinetic-plot-ribbon.svg

tests/testthat/_snaps/plot_replicate_histogram/replicates-histogram-one-time.svg

tests/testthat/_snaps/plot_replicate_histogram/replicates-histogram-all-time.svg

tests/testthat/_snaps/quality_control/quality-control-plot.svg

tests/testthat/_snaps/plot_overlap/overlap-plot.svg

tests/testthat/_snaps/plot_differential_butterfly/frac-differential-butterfly-plot-bars.svg

tests/testthat/_snaps/plot_differential_butterfly/theo-differential-butterfly-plot-bars.svg

tests/testthat/_snaps/plot_differential_butterfly/differential-butterfly-plot.svg

tests/testthat/_snaps/plot_differential_butterfly/hybrid-test.svg

tests/testthat/_snaps/create_overlap_distribution_dataset/overlap-distribution-plot.svg

tests/testthat/_snaps/plot_differential_chiclet/hybrid-test.svg

tests/testthat/_snaps/plot_differential_chiclet/differential-chiclet-plot.svg

tests/testthat/_snaps/plot_differential_chiclet/theo-differential-chiclet-plot.svg

tests/testthat/_snaps/plot_differential/differential-with-tstudent.svg

tests/testthat/_snaps/plot_differential/theo-frac-differential-plot.svg

tests/testthat/_snaps/plot_differential/skip-amino.svg

tests/testthat/_snaps/plot_differential/fractional-differential-plot.svg

tests/testthat/_snaps/plot_differential/differential-with-houde.svg

tests/testthat/_snaps/plot_differential/differential-plot-all-times.svg

tests/testthat/_snaps/plot_differential/insig-sig-tstud.svg

tests/testthat/_snaps/plot_differential/theoretical-differential-plot.svg

tests/testthat/_snaps/plot_differential_uptake_curve/theo-frac-diff-uc.svg

tests/testthat/_snaps/plot_differential_uptake_curve/no-logx.svg

tests/testthat/_snaps/plot_differential_uptake_curve/diff-uptake-curve.svg

tests/testthat/_snaps/plot_differential_uptake_curve/hybrid-test.svg

tests/testthat/_snaps/plot_differential_uptake_curve/frac-diff-uc.svg

tests/testthat/_snaps/plot_differential_uptake_curve/theo-diff-uc.svg

tests/testthat/_snaps/plot_replicate_mass_uptake/aggregated-plot.svg

tests/testthat/_snaps/plot_replicate_mass_uptake/replicate-mass-uptake-plot.svg

tests/testthat/_snaps/plot_coverage/plot-works.svg

tests/figs/deps.txt

tests/figs/woods-plot-in-test/woods-plot-2.svg

tests/figs/woods-plot-in-test/woods-plot-1.svg

tests/figs/plot-position-frequency-in-test/position-frequency-plot-1.svg

tests/figs/plot-coverage-in-test/graphic-overlapping-plot-1.svg

tests/figs/comparison-plot-in-test/comparison-plot-2.svg

tests/figs/comparison-plot-in-test/comparison-plot-1.svg

vignettes/transformation.Rmd vignettes/glossary.Rmd

vignettes/peptide_coverage-display_plot.svg

vignettes/statistics.Rmd

vignettes/butterfly-display_plot.svg

vignettes/seca_3d_vis.png

vignettes/differential_heatmap-display_plot.svg

vignettes/plt3.png

vignettes/comparison.csv

vignettes/hadex2_docs.bib

vignettes/differential_heatmap-display_plot.png

vignettes/datafiles.Rmd vignettes/example.Rmd

vignettes/chiclet-display_plot.png

vignettes/peptide_coverage-display_plot.png

vignettes/comparison-display_plot.svg

vignettes/data_input.Rmd vignettes/visualization.Rmd

vignettes/version_benchmark.rds

vignettes/usage.Rmd

vignettes/chiclet-display_plot.svg

vignettes/quality_control.Rmd

vignettes/du.PNG

vignettes/woods-display_plot.svg

vignettes/comparison-display_plot.png

vignettes/spline.PNG

vignettes/woods-display_plot.png

vignettes/butterfly-display_plot.png

vignettes/curves.PNG

vignettes/version_comparison.Rmd vignettes/mass_comparison.Rmd

data/alpha_dat.rda

man/validate_hdx_data.Rd man/plot_differential.Rd man/get_structure_color.Rd man/create_diff_uptake_dataset.Rd man/plot_uptake_curve.Rd man/show_aggregated_uptake_data.Rd man/plot_peptide_mass_measurement.Rd man/prepare_hdxviewer_export.Rd man/calculate_kinetics.Rd man/install_GUI.Rd man/calculate_aggregated_uptake.Rd man/plot_position_frequency.Rd man/plot_volcano.Rd man/create_replicate_dataset.Rd man/HaDeXify.Rd man/plot_aggregated_uptake_structure.Rd man/plot_aggregated_differential_uptake.Rd man/HaDeX2-package.Rd man/create_state_uptake_dataset.Rd man/plot_differential_butterfly.Rd man/show_p_diff_uptake_data.Rd man/create_aggregated_diff_uptake_dataset.Rd man/new_hdx_data.Rd man/add_stat_dependency.Rd man/calculate_peptide_kinetics.Rd man/get_n_replicates.Rd man/plot_overlap.Rd man/create_overlap_distribution_dataset.Rd man/plot_amino_distribution.Rd man/read_hdx.Rd man/is_GUI_installed.Rd man/calculate_MHP.Rd man/calculate_aggregated_diff_uptake.Rd man/show_overlap_data.Rd man/plot_quality_control.Rd man/calculate_exp_masses_per_replicate.Rd man/hdx_data.Rd man/show_diff_uptake_data_confidence.Rd man/calculate_p_value.Rd man/show_quality_control_data.Rd man/create_p_diff_uptake_dataset_with_confidence.Rd man/show_diff_uptake_data.Rd man/get_residue_positions.Rd man/show_uptake_data.Rd man/alpha_dat.Rd man/show_peptide_mass_measurement.Rd man/calculate_diff_uptake.Rd man/get_protein_redundancy.Rd man/create_control_dataset.Rd man/calculate_auc.Rd man/create_aggregated_uptake_dataset.Rd man/get_protein_coverage.Rd man/plot_peptide_charge_measurement.Rd man/create_kinetic_dataset.Rd man/create_p_diff_uptake_dataset.Rd man/show_replicate_histogram_data.Rd man/plot_differential_uptake_curve.Rd man/plot_state_comparison.Rd man/calculate_confidence_limit_values.Rd man/plot_manhattan.Rd man/show_uc_data.Rd man/calculate_aggregated_test_results.Rd man/show_summary_data.Rd man/update_hdexaminer_file.Rd man/plot_coverage.Rd man/plot_uncertainty.Rd man/plot_butterfly.Rd man/plot_replicate_mass_uptake.Rd man/calculate_state_uptake.Rd man/plot_chiclet.Rd man/plot_coverage_heatmap.Rd man/create_uptake_dataset.Rd man/plot_replicate_histogram.Rd man/show_coverage_heatmap_data.Rd man/get_peptide_sequence.Rd man/calculate_exp_masses.Rd man/get_replicate_list_sd.Rd man/create_state_comparison_dataset.Rd man/create_quality_control_dataset.Rd man/plot_differential_chiclet.Rd man/calculate_back_exchange.Rd man/plot_overlap_distribution.Rd man/reconstruct_sequence.Rd man/show_peptide_charge_measurement.Rd man/HaDeX_GUI.Rd man/plot_aggregated_uptake.Rd

HaDeX2 documentation built on Feb. 9, 2026, 5:07 p.m.