Index A | B | C | D | E | F | G | I | L | M | N | P | R | S | T | U | V A abudnance_unpaired_sig_thr (proteometer.params.Params attribute) abundance_correction (proteometer.params.Params attribute) abundance_correction_paired_samples (proteometer.params.Params attribute) AggDictFloat (in module proteometer.lip) (in module proteometer.rollup) analyze_tryptic_pattern() (in module proteometer.lip) anova() (in module proteometer.stats) anova_columns() (in module proteometer.parse_metadata) anova_factors (proteometer.params.Params attribute) B batch_correct_samples (proteometer.params.Params attribute) batch_correction (proteometer.params.Params attribute) batch_correction() (in module proteometer.normalization) biplot() (in module proteometer.quality_control_plots) C calculate_all_pairwise_scalars() (in module proteometer.stats) calculate_pairwise_scalars() (in module proteometer.stats) check_missingness() (in module proteometer.utils) combine_multi_ptms() (in module proteometer.ptm) control_group (proteometer.stats.TTestGroup attribute) control_samples (proteometer.stats.TTestGroup attribute) correlation_plot() (in module proteometer.quality_control_plots) count_site_number() (in module proteometer.residue) count_site_number_with_global_proteomics() (in module proteometer.residue) D data_dir (proteometer.params.Params attribute) delta_prok_site() (in module proteometer.lip) double_pept_file (proteometer.params.Params attribute) E experiment_col (proteometer.params.Params attribute) experiment_name (proteometer.params.Params attribute) experiment_type (proteometer.params.Params attribute) expsum() (in module proteometer.utils) F fasta_file (proteometer.params.Params attribute) filter_contaminants_reverse_pept() (in module proteometer.lip) filter_contaminants_reverse_prot() (in module proteometer.lip) filter_missingness() (in module proteometer.utils) filtering_protein_based_on_peptide_number() (in module proteometer.lip) flatten() (in module proteometer.utils) G generate_index() (in module proteometer.utils) get_barcode() (in module proteometer.barcode) get_clean_peptides() (in module proteometer.lip) get_df_for_pept_alignment_plot() (in module proteometer.alignment) get_phosphositeplus_pos() (in module proteometer.ptm) get_prot_abund_scalars() (in module proteometer.abundance) get_ptm_pos_in_pept() (in module proteometer.ptm) get_res_names() (in module proteometer.residue) get_res_pos() (in module proteometer.residue) get_sequences_from_fasta() (in module proteometer.fasta) get_tryptic_types() (in module proteometer.lip) get_yst() (in module proteometer.ptm) global_pept_file (proteometer.params.Params attribute) global_prot_file (proteometer.params.Params attribute) global_prot_normalization_and_stats() (in module proteometer.abundance) group_columns() (in module proteometer.parse_metadata) I id_col (proteometer.params.Params attribute) id_separator (proteometer.params.Params attribute) int_columns() (in module proteometer.parse_metadata) L label() (proteometer.stats.TTestGroup method) lip_analysis() (in module proteometer.lip_analysis) log2_scale (proteometer.params.Params attribute) log2_transformation() (in module proteometer.stats) M median_normalization() (in module proteometer.normalization) median_normalize_columns() (in module proteometer.normalization) metadata_batch_col (proteometer.params.Params attribute) metadata_condition_col (proteometer.params.Params attribute) metadata_control_condition (proteometer.params.Params attribute) metadata_file (proteometer.params.Params attribute) metadata_group_col (proteometer.params.Params attribute) metadata_sample_col (proteometer.params.Params attribute) metadata_treatment_condition (proteometer.params.Params attribute) min_pept_count (proteometer.params.Params attribute) min_replicates_qc (proteometer.params.Params attribute) module proteometer proteometer.abundance proteometer.alignment proteometer.barcode proteometer.fasta proteometer.lip proteometer.lip_analysis proteometer.normalization proteometer.params proteometer.parse_metadata proteometer.peptide proteometer.ptm proteometer.ptm_analysis proteometer.quality_control_plots proteometer.residue proteometer.rollup proteometer.stats proteometer.utils N nip_off_pept() (in module proteometer.peptide) P pairwise_ttest() (in module proteometer.stats) Params (class in proteometer.params) peptide_batch_correction() (in module proteometer.normalization) peptide_col (proteometer.params.Params attribute) peptide_normalization() (in module proteometer.normalization) peptide_normalization_and_correction() (in module proteometer.normalization) plot_barcode() (in module proteometer.barcode) plot_pept_alignment() (in module proteometer.alignment) plot_pept_barcode() (in module proteometer.barcode) plot_site_barcode() (in module proteometer.barcode) pooled_chanel_condition (proteometer.params.Params attribute) prot_abund_correction() (in module proteometer.abundance) prot_abund_correction_matched() (in module proteometer.abundance) prot_abund_correction_sig_only() (in module proteometer.abundance) protein_col (proteometer.params.Params attribute) proteometer module proteometer.abundance module proteometer.alignment module proteometer.barcode module proteometer.fasta module proteometer.lip module proteometer.lip_analysis module proteometer.normalization module proteometer.params module proteometer.parse_metadata module proteometer.peptide module proteometer.ptm module proteometer.ptm_analysis module proteometer.quality_control_plots module proteometer.residue module proteometer.rollup module proteometer.stats module proteometer.utils module ptm_abbreviations (proteometer.params.Params attribute) ptm_analysis() (in module proteometer.ptm_analysis) ptm_analysis_return_all() (in module proteometer.ptm_analysis) ptm_names (proteometer.params.Params attribute) ptm_pept_files (proteometer.params.Params attribute) ptm_symbols (proteometer.params.Params attribute) R recalculate_adj_pval() (in module proteometer.stats) recalculate_adj_pval_proteinwise() (in module proteometer.stats) residue_col (proteometer.params.Params attribute) result_dir (proteometer.params.Params attribute) rollup_single_protein_to_lytic_site() (in module proteometer.lip) rollup_to_lytic_site() (in module proteometer.lip) rollup_to_site() (in module proteometer.rollup) S search_tool (proteometer.params.Params attribute) select_lytic_sites() (in module proteometer.lip) select_tryptic_pattern() (in module proteometer.lip) sig_thr (proteometer.params.Params attribute) sig_type (proteometer.params.Params attribute) site_col (proteometer.params.Params attribute) site_number_col (proteometer.params.Params attribute) strip_peptide() (in module proteometer.peptide) T t_test_groups() (in module proteometer.parse_metadata) tmt_normalization() (in module proteometer.normalization) treat_group (proteometer.stats.TTestGroup attribute) treat_samples (proteometer.stats.TTestGroup attribute) ttest_pairs (proteometer.params.Params attribute) TTestGroup (class in proteometer.stats) type_col (proteometer.params.Params attribute) U uniprot_col (proteometer.params.Params attribute) V volcano_plot() (in module proteometer.quality_control_plots)