ionique

Contents:

  • Nanopore Signal Analysis Framework
    • Signal Preprocessing
      • Filtering with Filter class
      • Trimming with Trimmer class
      • Summary
    • Signal Analysis
    • Data Input
  • API Reference
    • ionique.io
      • AbstractFileReader
        • AbstractFileReader.__init__()
        • AbstractFileReader.accepted_keywords
        • AbstractFileReader.current_multiplier
        • AbstractFileReader.ext
        • AbstractFileReader.read()
        • AbstractFileReader.voltage_multiplier
      • EDHReader
        • EDHReader.__init__()
        • EDHReader.accepted_keywords
        • EDHReader.current_multiplier
        • EDHReader.ext
        • EDHReader.voltage_multiplier
      • OPTReader
        • OPTReader.__init__()
        • OPTReader.accepted_keywords
        • OPTReader.current_multiplier
        • OPTReader.ext
        • OPTReader.find_peaks_in_segment()
        • OPTReader.find_peaks_slide_window()
        • OPTReader.process_custom_xml()
      • load_files_GUI()
      • select_files_GUI()
    • ionique.core
      • AbstractSegmentTree
        • AbstractSegmentTree.__init__()
        • AbstractSegmentTree.add_child()
        • AbstractSegmentTree.add_children()
        • AbstractSegmentTree.children
        • AbstractSegmentTree.clear_children()
        • AbstractSegmentTree.climb_to_rank()
        • AbstractSegmentTree.end
        • AbstractSegmentTree.get_feature()
        • AbstractSegmentTree.get_top_parent()
        • AbstractSegmentTree.n
        • AbstractSegmentTree.parent
        • AbstractSegmentTree.parse()
        • AbstractSegmentTree.rank
        • AbstractSegmentTree.relative_end
        • AbstractSegmentTree.relative_slice
        • AbstractSegmentTree.relative_start
        • AbstractSegmentTree.slice
        • AbstractSegmentTree.start
        • AbstractSegmentTree.traverse_to_rank()
      • MetaSegment
        • MetaSegment.__init__()
        • MetaSegment.current
        • MetaSegment.delete()
        • MetaSegment.duration
        • MetaSegment.from_json()
        • MetaSegment.max
        • MetaSegment.mean
        • MetaSegment.min
        • MetaSegment.std
        • MetaSegment.time
        • MetaSegment.to_dict()
        • MetaSegment.to_json()
        • MetaSegment.to_meta()
        • MetaSegment.unique_features
      • Segment
        • Segment.__init__()
        • Segment.children
        • Segment.delete()
        • Segment.end
        • Segment.from_json()
        • Segment.max
        • Segment.mean
        • Segment.min
        • Segment.n
        • Segment.parent
        • Segment.rank
        • Segment.scale()
        • Segment.start
        • Segment.std
        • Segment.to_dict()
        • Segment.to_json()
        • Segment.to_meta()
      • ignored()
    • ionique.parsers
      • AutoSquareParser
        • AutoSquareParser.__init__()
        • AutoSquareParser.parse()
        • AutoSquareParser.required_parent_attributes
      • FilterDerivativeSegmenter
        • FilterDerivativeSegmenter.__init__()
        • FilterDerivativeSegmenter.parse()
        • FilterDerivativeSegmenter.set_params()
      • IVCurveAnalyzer
        • IVCurveAnalyzer.__init__()
        • IVCurveAnalyzer.analyze()
      • IVCurveParser
        • IVCurveParser.__init__()
        • IVCurveParser.parse()
      • MemoryParse
        • MemoryParse.__init__()
        • MemoryParse.parse()
      • NoiseFilterParser
        • NoiseFilterParser.__init__()
        • NoiseFilterParser.parse()
      • Parser
        • Parser.__init__()
        • Parser.from_json()
        • Parser.get_init_params()
        • Parser.get_name()
        • Parser.get_process_inputs()
        • Parser.get_process_outputs()
        • Parser.get_required_parent_attributes()
        • Parser.parse()
        • Parser.required_parent_attributes
        • Parser.set_params()
        • Parser.to_dict()
        • Parser.to_json()
      • SpeedyStatSplit
        • SpeedyStatSplit.__init__()
        • SpeedyStatSplit.best_single_split()
        • SpeedyStatSplit.parse()
        • SpeedyStatSplit.parse_meta()
        • SpeedyStatSplit.set_params()
        • SpeedyStatSplit.uiTemplate
      • SpikeParser
        • SpikeParser.__init__()
        • SpikeParser.parse()
        • SpikeParser.required_parent_attributes
      • lambda_event_parser
        • lambda_event_parser.__init__()
        • lambda_event_parser.parse()
        • lambda_event_parser.set_params()
      • pairwise()
      • snakebase_parser
        • snakebase_parser.__init__()
        • snakebase_parser.parse()
        • snakebase_parser.set_params()
    • ionique.utils
      • Filter
        • Filter.__init__()
        • Filter.bidirectional
        • Filter.cutoff_frequency
        • Filter.filter_method
        • Filter.filter_type
        • Filter.sampling_frequency
      • Singleton
        • Singleton.__init__()
      • Trimmer
        • Trimmer.__init__()
        • Trimmer.newrank
        • Trimmer.rank
        • Trimmer.samples_to_remove
      • extract_features()
      • si_eval()
      • split_voltage_steps()
    • ionique.datatypes
      • SessionFileManager
        • SessionFileManager.__init__()
        • SessionFileManager.add_child()
        • SessionFileManager.add_children()
        • SessionFileManager.rank
        • SessionFileManager.register_affector()
        • SessionFileManager.unique_features
      • TraceFile
        • TraceFile.__init__()
        • TraceFile.children
        • TraceFile.delete()
        • TraceFile.end
        • TraceFile.parent
        • TraceFile.plot()
        • TraceFile.rank
        • TraceFile.start
    • ionique.cparsers
      • FastStatSplit
        • FastStatSplit.__init__()
        • FastStatSplit.best_single_split()
        • FastStatSplit.min_gain
        • FastStatSplit.parse()
        • FastStatSplit.parse_meta()
        • FastStatSplit.score_samples()
      • pairwise()

Guides

  • Installation for beginners
    • Welcome to Ionique!
    • Step 1: Install Python
    • Step 2: GitHub
    • Step 3: Moving Between Folders in the Terminal
    • Step 4: Virtual Environment
    • Step 5: Run the Notebooks
    • Step 6: Finish Workflow
  • Install Ionique
    • 1. Download the Ionique Repository
    • 2. Open the Ionique Folder in VS Code
    • 3. Set Up a Virtual Environment
      • Step 1: Open Terminal in VS Code
      • Step 2: Confirm You’re in the Correct Directory
      • Step 3: Create and Activate the Environment
    • 4. Install the Ionique Package
    • 5. (Optional) Install JupyterLab
    • 6. Deactivate the Environment
  • Guide for VSCode and Python Installation
    • Installing VS Code
      • 1. Install VS Code
      • 2. Install Required Extensions
      • 3. Install Compilers (Build Tools)
      • 4. Install Python.
        • Skip this step if you already have Python!
      • 1. Download and Install VS_Code
      • 2. Open a Terminal
      • 3. Install Python
        • Skip this step if you already have Python!
      • 1. Install VS Code
      • 2. Install Python
        • Skip this step if you already have Python!
ionique
  • Nanopore Signal Analysis Framework
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© Copyright 2025, Ali Fallahi, Dinara Boyko, Wanunu Lab.

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