Index _ | A | C | D | E | F | H | I | L | M | N | P | R | S | T | U _ __init__() (omicspylib.analysis.clusters.HierarchicallyClusteredHeatmap method) (omicspylib.analysis.pairs.frequency_based.PairwiseUniqueEntryComparison method) (omicspylib.analysis.pairs.statistical.PairwiseComparisonTTestFC method) (omicspylib.datasets.peptides.PeptidesDataset method) (omicspylib.datasets.peptides.PeptidesDatasetExpCondition method) (omicspylib.datasets.proteins.ProteinsDataset method) (omicspylib.datasets.proteins.ProteinsDatasetExpCondition method) A append() (omicspylib.datasets.peptides.PeptidesDataset method) (omicspylib.datasets.proteins.ProteinsDataset method) C calc_fold_change() (in module omicspylib.calculations.fold_change) calc_ttest_adj() (in module omicspylib.calculations.ttest) condition_names (omicspylib.datasets.peptides.PeptidesDataset attribute) (omicspylib.datasets.proteins.ProteinsDataset attribute) D describe() (omicspylib.datasets.peptides.PeptidesDataset method) (omicspylib.datasets.peptides.PeptidesDatasetExpCondition method) (omicspylib.datasets.proteins.ProteinsDataset method) (omicspylib.datasets.proteins.ProteinsDatasetExpCondition method) drop() (omicspylib.datasets.peptides.PeptidesDataset method) (omicspylib.datasets.peptides.PeptidesDatasetExpCondition method) (omicspylib.datasets.proteins.ProteinsDataset method) (omicspylib.datasets.proteins.ProteinsDatasetExpCondition method) E eval() (omicspylib.analysis.clusters.HierarchicallyClusteredHeatmap method) (omicspylib.analysis.pairs.frequency_based.PairwiseUniqueEntryComparison method) (omicspylib.analysis.pairs.statistical.PairwiseComparisonTTestFC method) experiment_names (omicspylib.datasets.peptides.PeptidesDatasetExpCondition attribute) (omicspylib.datasets.proteins.ProteinsDatasetExpCondition attribute) experiment_names() (omicspylib.datasets.peptides.PeptidesDataset method) (omicspylib.datasets.proteins.ProteinsDataset method) F filter() (omicspylib.datasets.peptides.PeptidesDataset method) (omicspylib.datasets.peptides.PeptidesDatasetExpCondition method) (omicspylib.datasets.proteins.ProteinsDataset method) (omicspylib.datasets.proteins.ProteinsDatasetExpCondition method) frequency() (omicspylib.datasets.peptides.PeptidesDataset method) (omicspylib.datasets.peptides.PeptidesDatasetExpCondition method) (omicspylib.datasets.proteins.ProteinsDataset method) (omicspylib.datasets.proteins.ProteinsDatasetExpCondition method) from_df() (omicspylib.datasets.peptides.PeptidesDataset class method) (omicspylib.datasets.proteins.ProteinsDataset class method) from_maxquant() (omicspylib.datasets.proteins.ProteinsDataset class method) H HierarchicallyClusteredHeatmap (class in omicspylib.analysis.clusters) I id_col (omicspylib.datasets.peptides.PeptidesDatasetExpCondition attribute) (omicspylib.datasets.proteins.ProteinsDatasetExpCondition attribute) impute() (omicspylib.datasets.peptides.PeptidesDataset method) (omicspylib.datasets.peptides.PeptidesDatasetExpCondition method) (omicspylib.datasets.proteins.ProteinsDataset method) (omicspylib.datasets.proteins.ProteinsDatasetExpCondition method) L log2_backtransform() (omicspylib.datasets.peptides.PeptidesDataset method) (omicspylib.datasets.peptides.PeptidesDatasetExpCondition method) (omicspylib.datasets.proteins.ProteinsDataset method) (omicspylib.datasets.proteins.ProteinsDatasetExpCondition method) log2_transform() (omicspylib.datasets.peptides.PeptidesDataset method) (omicspylib.datasets.peptides.PeptidesDatasetExpCondition method) (omicspylib.datasets.proteins.ProteinsDataset method) (omicspylib.datasets.proteins.ProteinsDatasetExpCondition method) M mean() (omicspylib.datasets.peptides.PeptidesDataset method) (omicspylib.datasets.peptides.PeptidesDatasetExpCondition method) (omicspylib.datasets.proteins.ProteinsDataset method) (omicspylib.datasets.proteins.ProteinsDatasetExpCondition method) metadata (omicspylib.datasets.peptides.PeptidesDatasetExpCondition attribute) (omicspylib.datasets.proteins.ProteinsDatasetExpCondition attribute) min() (omicspylib.datasets.peptides.PeptidesDatasetExpCondition method) (omicspylib.datasets.proteins.ProteinsDatasetExpCondition method) missing_values() (omicspylib.datasets.peptides.PeptidesDataset method) (omicspylib.datasets.peptides.PeptidesDatasetExpCondition method) (omicspylib.datasets.proteins.ProteinsDataset method) (omicspylib.datasets.proteins.ProteinsDatasetExpCondition method) mq_rm_contaminants() (in module omicspylib.utils.mq) mq_rm_only_modified() (in module omicspylib.utils.mq) mq_rm_reverse() (in module omicspylib.utils.mq) N n_conditions (omicspylib.datasets.peptides.PeptidesDataset attribute) (omicspylib.datasets.proteins.ProteinsDataset attribute) n_experiments (omicspylib.datasets.peptides.PeptidesDataset attribute) (omicspylib.datasets.peptides.PeptidesDatasetExpCondition attribute) (omicspylib.datasets.proteins.ProteinsDataset attribute) (omicspylib.datasets.proteins.ProteinsDatasetExpCondition attribute) n_records (omicspylib.datasets.peptides.PeptidesDataset attribute) (omicspylib.datasets.proteins.ProteinsDataset attribute) name (omicspylib.datasets.peptides.PeptidesDatasetExpCondition attribute) (omicspylib.datasets.proteins.ProteinsDatasetExpCondition attribute) normalize() (omicspylib.datasets.peptides.PeptidesDataset method) (omicspylib.datasets.proteins.ProteinsDataset method) P PairwiseComparisonTTestFC (class in omicspylib.analysis.pairs.statistical) PairwiseUniqueEntryComparison (class in omicspylib.analysis.pairs.frequency_based) PeptidesDataset (class in omicspylib.datasets.peptides) PeptidesDatasetExpCondition (class in omicspylib.datasets.peptides) plot_density() (in module omicspylib.plots.density) plot_missing_values() (in module omicspylib.plots.missing_values) plot_venn2() (in module omicspylib.plots.venn) plot_volcano() (in module omicspylib.plots.volcano) ProteinsDataset (class in omicspylib.datasets.proteins) ProteinsDatasetExpCondition (class in omicspylib.datasets.proteins) R record_ids (omicspylib.datasets.peptides.PeptidesDatasetExpCondition attribute) (omicspylib.datasets.proteins.ProteinsDatasetExpCondition attribute) S shift() (omicspylib.datasets.peptides.PeptidesDatasetExpCondition method) (omicspylib.datasets.proteins.ProteinsDatasetExpCondition method) T to_table() (omicspylib.datasets.peptides.PeptidesDataset method) (omicspylib.datasets.peptides.PeptidesDatasetExpCondition method) (omicspylib.datasets.proteins.ProteinsDataset method) (omicspylib.datasets.proteins.ProteinsDatasetExpCondition method) U unique_records() (omicspylib.datasets.peptides.PeptidesDataset method) (omicspylib.datasets.proteins.ProteinsDataset method)