PhysioCore - Core Data Structures for Physiological Signal Analysis

Provides the PhysioExperiment class, a SummarizedExperiment extension for multi-modal physiological signal data. Includes core accessors, channel and event management, and basic S4 methods. Designed as a lightweight foundation for the Physio ecosystem.

Last updated

4.38 score 8 dependents

PhysioEEG - EEG Analysis Functions for PhysioExperiment Objects

Provides comprehensive electroencephalography (EEG) analysis functions for PhysioExperiment objects. Includes preprocessing (filtering, re-referencing, bad channel detection, interpolation, epoching, artifact rejection), independent component analysis (FastICA, Infomax, JADE) with automatic artifact detection, event-related potential (ERP) component detection and measurement (N100, P300, N400, P600, MMN), source localization (eLORETA, sLORETA, LCMV beamformer), EEG microstate analysis (K-means, AAHC), sleep staging (AASM criteria, spindle/K-complex/slow-wave detection), brain-computer interface features (CSP, SSVEP, motor imagery), clinical EEG analysis (spike detection, QEEG, asymmetry indices), time-frequency analysis (Morlet wavelet, STFT, multitaper, ERSP, ITC), connectivity analysis (coherence, PLV, wPLI, Granger causality), visualization (signal traces, ERP waveforms, topographic maps, spectrograms, connectivity plots, hypnograms, source maps), and simulated data generators for testing and demonstration.

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3.65 score

PhysioMoCap - Motion Capture and Biomechanics Analysis for PhysioExperiment Objects

Provides motion capture, pose estimation, and biomechanical simulation analysis for PhysioExperiment objects. Includes I/O for C3D, Venus3D, GaitRec, OpenPose, DeepLabCut, MediaPipe, BVH, ASF/AMC, OpenSim, and generic CSV formats. Provides marker tracking (Hungarian algorithm), signal filtering, numerical differentiation, resampling, center of mass calculation, gait parameters, clinical statistics (ICC, SEM, MDC, Bland-Altman), movement phase segmentation, dynamic time warping, movement normalization, functional PCA, force-plate kinetics (GRF filtering, COP, loading rate, impulse), planar inverse dynamics (joint moments/power), EMG integration (rectification, RMS envelope, MVC normalization), gait/running/jump task schemas, OpenSim workflow integration, and biomechanics-specific visualization.

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3.40 score

PhysioOpenSim - Native OpenSim C++ Integration for PhysioExperiment

Provides a native OpenSim C++ bridge for R via Rcpp. The package exposes OpenSim model-level operations to support biomechanics workflows in the Physio ecosystem. OpenSim linkage is optional at build time; when OpenSim is not detected, the package installs with informative runtime errors for OpenSim-dependent calls.

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cpp

3.00 score

PhysioCrossModal - Cross-Modal Coupling Analysis for PhysioExperiment Objects

Provides cross-modal coupling, connectivity, and synchrony analysis between physiological signals of different modalities (EEG, EMG, ECG, EDA, MoCap, fNIRS, etc.). Introduces a MultiPhysioExperiment container class for holding multiple PhysioExperiment objects at different sampling rates with temporal alignment. Includes spectral coherence, phase synchrony (PLV, PLI, wPLI), directed coupling (Granger causality), and time-domain coupling (cross-correlation) methods.

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3.00 score

PhysioECG - ECG Analysis Functions for PhysioExperiment Objects

Provides electrocardiography (ECG) analysis functions for PhysioExperiment objects. Includes R-peak detection (adaptive Pan-Tompkins), RR interval computation, HRV time-domain metrics (SDNN, RMSSD, pNN50), HRV frequency-domain analysis (VLF, LF, HF power), nonlinear HRV (Poincare, Sample Entropy, DFA), ECG morphology analysis (QRS boundaries, QT/QTc intervals), and signal quality assessment with ectopic beat correction.

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3.00 score

PhysioEMG - EMG Analysis Functions for PhysioExperiment Objects

Provides electromyography (EMG) analysis functions for PhysioExperiment objects. Includes envelope extraction (RMS, Hilbert), muscle activation onset detection (Hodges-Bui, Teager-Kaiser), fatigue analysis (median frequency shift), and muscle synergy decomposition (NMF, PCA, ICA).

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3.00 score

PhysioAnalysis - Analysis and Visualization for PhysioExperiment Objects

Provides analysis and visualization functions for physiological signal data including FFT, time-frequency analysis, epoching, connectivity analysis, statistical testing, and various plotting functions including topoplots and multichannel displays.

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3.00 score

PhysioPreprocess - Preprocessing Functions for PhysioExperiment Objects

Provides preprocessing functions for physiological signal data including digital filters (Butterworth, notch), resampling, artifact detection, ICA-based artifact removal, and preprocessing pipelines.

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3.00 score

PhysioIO - I/O Functions for PhysioExperiment Objects

Provides comprehensive I/O capabilities for PhysioExperiment objects. Supports EDF/EDF+, HDF5, BIDS, CSV, MATLAB formats, and DuckDB database integration. Includes out-of-memory processing for large datasets via HDF5Array.

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3.00 score

PhysioExperiment - Unified Analysis of Physiological Signals

A comprehensive R/Bioconductor framework for physiological signal analysis. Provides a unified data model (PhysioExperiment class extending SummarizedExperiment) for multi-modal sensor signals (EEG, EMG, ECG, IMU, MoCap). Includes file I/O (EDF, BDF, BrainVision, GDF, HDF5, BIDS, CSV, MATLAB), database integration (DuckDB), signal preprocessing (filtering, artifact removal, epoching), time-frequency analysis, connectivity analysis, network metrics, statistical testing (SPM1D, permutation tests), and publication-quality visualization.

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softwaretimecoursepreprocessingopenblascppopenmp

2.70 score

PhysioAnnotationHub - Anatomical and Clinical Knowledge Graph for Physiological Data

Centralized annotation hub providing anatomical ontology, muscle/bone metadata, nerve innervation, clinical codes (ICD-10, ICF), and knowledge graph queries for the physio-ecosystem.

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1.70 score

PhysioMSKNet - Musculoskeletal Network Analysis for Physiological Data

Network science analysis of the human musculoskeletal system. Implements hypergraph representations of muscle-bone connections, physical simulation via damped harmonic oscillators, perturbation-based impact scoring, community detection, and clinical outcome prediction. Based on Murphy et al. (2018) <doi:10.1371/journal.pbio.2002811>.

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1.70 score