Method List
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#add_parameter Macroape::CLI::OutputInformation
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#add_resulting_value Macroape::CLI::OutputInformation
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#add_table_parameter Macroape::CLI::OutputInformation
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#add_table_parameter_without_description Macroape::CLI::OutputInformation
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#alignment_infos Macroape::PWMCompareAligned
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#background_parameter Macroape::CLI::OutputInformation
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calculate_alignment_length Macroape::PWMCompareAligned
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#count_by_threshold Bioinform::PWM
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#count_distribution Bioinform::PWM
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#count_distribution_after_threshold Bioinform::PWM
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#count_distribution_under_pvalue Bioinform::PWM
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#counts_by_thresholds Bioinform::PWM
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#counts_for_two_matrices Macroape::PWMCompareAligned
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#direct? Macroape::PWMCompareAligned
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#each_alignment Macroape::PWMCompare
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find_pvalue_info_string Macroape::CLI::Helper
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#first Macroape::PWMCompareAligned
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#first Macroape::PWMCompare
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#first_length Macroape::PWMCompareAligned
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#first_overlaps? Macroape::PWMCompareAligned
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#first_pwm_alignment Macroape::PWMCompareAligned
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#get_counts Macroape::PWMCompareAligned
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#header_content Macroape::CLI::OutputInformation
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#initialize Macroape::PWMCompareAligned
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#initialize Macroape::PWMCompare
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#initialize Macroape::CLI::OutputInformation
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#jaccard Macroape::PWMCompareAligned
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#jaccard Macroape::PWMCompare
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#jaccard_by_pvalue Macroape::PWMCompareAligned
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#jaccard_by_pvalue Macroape::PWMCompare
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#jaccard_by_weak_pvalue Macroape::PWMCompareAligned
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#jaccard_by_weak_pvalue Macroape::PWMCompare
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#length Macroape::PWMCompareAligned
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main Macroape::CLI::PreprocessCollection
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main Macroape::CLI::FindThreshold
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main Macroape::CLI::ScanCollection
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main Macroape::CLI::EvalAlignment
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main Macroape::CLI::AlignMotifs
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main Macroape::CLI::EvalSimilarity
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main Macroape::CLI::FindPValue
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#orientation Macroape::PWMCompareAligned
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#overlap Macroape::PWMCompareAligned
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#parameter_description_string Macroape::CLI::OutputInformation
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#parameters Macroape::PWMCompare
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#parameters Macroape::PWMCompareAligned
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#parameters_info Macroape::CLI::OutputInformation
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#pvalue_by_threshold Bioinform::PWM
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#recalc_score_hash Bioinform::PWM
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#recalc_score_hash Macroape::PWMCompareAligned
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#result Macroape::CLI::OutputInformation
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#resulting_table Macroape::CLI::OutputInformation
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#resulting_values_info Macroape::CLI::OutputInformation
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#revcomp? Macroape::PWMCompareAligned
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#run_tool_cmd Module
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scan_collection_infos_string Macroape::CLI::Helper
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#second Macroape::PWMCompare
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#second Macroape::PWMCompareAligned
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#second_length Macroape::PWMCompareAligned
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#second_overlaps? Macroape::PWMCompareAligned
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#second_pwm_alignment Macroape::PWMCompareAligned
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#shift Macroape::PWMCompareAligned
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similarity_info_string Macroape::CLI::Helper
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#snake_case String
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#table_content Macroape::CLI::OutputInformation
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#threshold Bioinform::PWM
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#threshold_and_real_pvalue Bioinform::PWM
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threshold_infos_string Macroape::CLI::Helper
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#thresholds Bioinform::PWM
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#thresholds_by_pvalues Bioinform::PWM
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#tool_name Module
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#weak_threshold Bioinform::PWM
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#weak_threshold_and_real_pvalue Bioinform::PWM
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#weak_thresholds Bioinform::PWM