Index

_

__init__() (mspypeline.BasePlotter method) (mspypeline.BaseReader method) (mspypeline.DataNode method) (mspypeline.DataTree method) (mspypeline.helpers.Utils.DataDict method) (mspypeline.MaxQuantPlotter method) (mspypeline.MedianNormalizer method) (mspypeline.modules.Normalization.BaseNormalizer method) (mspypeline.MQReader method) (mspypeline.MSPGUI method) (mspypeline.MSPInitializer method) (mspypeline.plotting_backend.matplotlib_plots.QuantileNormalize method) (mspypeline.QuantileNormalizer method) (mspypeline.TailRobustNormalizer method) (mspypeline.UIHandler method)

A

add_data() (mspypeline.DataTree method) add_intensity_column() (mspypeline.BasePlotter method) add_normalized_option() (mspypeline.BasePlotter method)

aggregate() (mspypeline.DataNode method) (mspypeline.DataTree method) aggregate_technical_replicates() (mspypeline.DataTree method)

B

BaseNormalizer (class in mspypeline.modules.Normalization)

BasePlotter (class in mspypeline) BaseReader (class in mspypeline)

C

configs (mspypeline.MSPInitializer attribute)

create_report() (mspypeline.MaxQuantPlotter method) create_results() (mspypeline.BasePlotter method)

D

DataDict (class in mspypeline.helpers.Utils)

DataNode (class in mspypeline) DataTree (class in mspypeline)

F

file_path_yaml() (mspypeline.MSPInitializer property) fit() (mspypeline.MedianNormalizer method) (mspypeline.modules.Normalization.BaseNormalizer method) (mspypeline.QuantileNormalizer method) (mspypeline.TailRobustNormalizer method)

fit_transform() (mspypeline.modules.Normalization.BaseNormalizer method) from_analysis_design() (mspypeline.DataTree class method) from_file_reader() (mspypeline.BasePlotter class method) (mspypeline.MaxQuantPlotter class method) from_MSPInitializer() (mspypeline.BasePlotter class method) (mspypeline.MaxQuantPlotter class method)

G

get_boxplot_data() (mspypeline.BasePlotter method) get_detected_proteins_per_replicate_data() (mspypeline.BasePlotter method) get_detection_counts_data() (mspypeline.BasePlotter method) get_experiment_comparison_data() (mspypeline.BasePlotter method) get_go_analysis_data() (mspypeline.BasePlotter method) get_intensity_heatmap_data() (mspypeline.BasePlotter method) get_intensity_histograms_data() (mspypeline.BasePlotter method) get_intersection_and_unique() (in module mspypeline.helpers.Utils) get_kde_data() (mspypeline.BasePlotter method) get_legend_elements() (in module mspypeline.helpers.Utils) get_logger() (in module mspypeline.helpers) get_n_protein_vs_quantile_data() (mspypeline.BasePlotter method)

get_path_and_name_from_kwargs() (in module mspypeline.plotting_backend.matplotlib_plots) get_pathway_analysis_data() (mspypeline.BasePlotter method) get_pca_data() (mspypeline.BasePlotter method) get_plot_name_suffix() (in module mspypeline.helpers.Utils) get_r_volcano_data() (mspypeline.BasePlotter method) get_rank_data() (mspypeline.BasePlotter method) get_relative_std_data() (mspypeline.BasePlotter method) get_scatter_replicates_data() (mspypeline.BasePlotter method) get_total_number_children() (mspypeline.DataNode method) get_venn_data_per_key() (mspypeline.BasePlotter method) get_venn_group_data() (mspypeline.BasePlotter method) groupby() (mspypeline.DataNode method) (mspypeline.DataTree method)

I

init_config() (mspypeline.MSPInitializer method)

interpolate_data() (in module mspypeline)

L

level_keys_full_name (mspypeline.DataTree attribute)

M

MaxQuantPlotter (class in mspypeline) MedianNormalizer (class in mspypeline) module mspypeline.helpers.Utils mspypeline.plotting_backend.matplotlib_plots MQReader (class in mspypeline)

MSPGUI (class in mspypeline) MSPInitializer (class in mspypeline) MSPParser (class in mspypeline) mspypeline.helpers.Utils module mspypeline.plotting_backend.matplotlib_plots module

P

plot_all_normalizer_overview() (mspypeline.BasePlotter method) plot_annotate_line() (in module mspypeline.helpers.Utils) plot_boxplot() (mspypeline.BasePlotter method) plot_detected_proteins_per_replicate() (mspypeline.BasePlotter method) plot_detection_counts() (mspypeline.BasePlotter method) plot_experiment_comparison() (mspypeline.BasePlotter method) plot_go_analysis() (mspypeline.BasePlotter method) plot_heatmap_overview_all_normalizers() (mspypeline.BasePlotter method) plot_intensity_heatmap() (mspypeline.BasePlotter method) plot_intensity_histograms() (mspypeline.BasePlotter method) plot_kde() (mspypeline.BasePlotter method) plot_n_proteins_vs_quantile() (mspypeline.BasePlotter method) plot_normalization_overview() (mspypeline.BasePlotter method) plot_normalization_overview_all_normalizers() (mspypeline.BasePlotter method) plot_pathway_analysis() (mspypeline.BasePlotter method) plot_pathway_timecourse() (mspypeline.BasePlotter method)

plot_pca_overview() (mspypeline.BasePlotter method) plot_r_volcano() (mspypeline.BasePlotter method) plot_rank() (mspypeline.BasePlotter method) plot_relative_std() (mspypeline.BasePlotter method) plot_scatter_replicates() (mspypeline.BasePlotter method) plot_venn_groups() (mspypeline.BasePlotter method) plot_venn_results() (mspypeline.BasePlotter method) plotter (mspypeline.MQReader attribute) preprocess_contaminants() (mspypeline.MQReader method) preprocess_evidence() (mspypeline.MQReader method) preprocess_msmsScans() (mspypeline.MQReader method) preprocess_msScans() (mspypeline.MQReader method) preprocess_parameters() (mspypeline.MQReader method) preprocess_peptides() (mspypeline.MQReader method) preprocess_proteinGroups() (mspypeline.MQReader method) preprocess_summary() (mspypeline.MQReader method)

Q

QuantileNormalize (class in mspypeline.plotting_backend.matplotlib_plots)

QuantileNormalizer (class in mspypeline)

R

read_data() (mspypeline.MSPInitializer method)

root (mspypeline.DataTree attribute)

S

save_bar_venn() (in module mspypeline.plotting_backend.matplotlib_plots) save_boxplot_results() (in module mspypeline.plotting_backend.matplotlib_plots) save_correlation_heatmap_results() (in module mspypeline.plotting_backend.matplotlib_plots) save_csvs() (in module mspypeline.plotting_backend.matplotlib_plots) save_detected_proteins_per_replicate_results() (in module mspypeline.plotting_backend.matplotlib_plots) save_detection_counts_results() (in module mspypeline.plotting_backend.matplotlib_plots) save_experiment_comparison_results() (in module mspypeline.plotting_backend.matplotlib_plots) save_go_analysis_results() (in module mspypeline.plotting_backend.matplotlib_plots) save_intensities_heatmap_result() (in module mspypeline.plotting_backend.matplotlib_plots) save_intensity_histogram_results() (in module mspypeline.plotting_backend.matplotlib_plots) save_kde_results() (in module mspypeline.plotting_backend.matplotlib_plots)

save_n_proteins_vs_quantile_results() (in module mspypeline.plotting_backend.matplotlib_plots) save_normalization_overview_results() (in module mspypeline.plotting_backend.matplotlib_plots) save_pathway_analysis_results() (in module mspypeline.plotting_backend.matplotlib_plots) save_pathway_timecourse_results() (in module mspypeline.plotting_backend.matplotlib_plots) save_pca_results() (in module mspypeline.plotting_backend.matplotlib_plots) save_plot() (in module mspypeline.plotting_backend.matplotlib_plots) save_plot_func() (in module mspypeline.plotting_backend.matplotlib_plots) save_rank_results() (in module mspypeline.plotting_backend.matplotlib_plots) save_relative_std_results() (in module mspypeline.plotting_backend.matplotlib_plots) save_scatter_replicates_results() (in module mspypeline.plotting_backend.matplotlib_plots) save_venn() (in module mspypeline.plotting_backend.matplotlib_plots) save_volcano_results() (in module mspypeline.plotting_backend.matplotlib_plots)

T

TailRobustNormalizer (class in mspypeline) transform() (mspypeline.MedianNormalizer method) (mspypeline.modules.Normalization.BaseNormalizer method) (mspypeline.QuantileNormalizer method) (mspypeline.TailRobustNormalizer method)

U

UIHandler (class in mspypeline)