A comprehensive package for solid state nanopore data analysis and visualization.
Project description
Nanosense
Nanosense is a powerful and comprehensive Python package designed for analyzing and visualizing nanopore data. It provides a suite of 12 applications that offer a wide range of tools and functionalities to facilitate the exploration, processing, and interpretation of nanopore measurements.
Features
- Plotting and Selecting: Plot
.abf
and.hdf5
files, apply low-pass filters, and select specific parts of the file based on various conditions. - Data Reduction: Reduce nanopore data, perform event fitting, standardization, and ML-based data reduction using parallel processing.
- Data Visualization: Plot data files, perform PCA analysis, generate correlation matrices, and create density plots.
- Frequency and Multiplots: Plot data from different files, calculate the frequency of events per second, and filter data using various filters.
- Event Analysis: Analyze individual events in nanopore data and extract meaningful information.
- Combine Datasets: Merge datasets from data reduction or ML data obtained from different files.
- Clustering and Data Reduction: Cluster events and perform data reduction on individual events for both ML and normal analysis.
- ML Analysis: Train and test different ensemble-based and deep learning-based classifiers on nanopore data.
- Spectrogram and PSD: Calculate and plot spectrograms and Power Spectral Density (PSD) for selected data.
- Nanopore Size Calculation: Determine the size of nanopores based on conductance and solution conductivity measurements.
- Resource Monitor: Monitor the utilization of computer resources, including GPU, CPU cores, and RAM.
- Reduction Settings Viewer: Easily view and review the settings used for data reduction.
Installation
You can install Nanosense using pip:
pip install nanosense
Usage
To get started with Nanosense, simply import the package in your Python script:
import nanosense
Contributing
Contributions to Nanosense are welcome! If you encounter any issues, have suggestions for improvements, or would like to contribute new features, please open an issue or submit a pull request on the GitHub repository.
License
Nanosense is open-source software released under the MIT License.
Contact
For any questions or inquiries, please contact Shankar Dutt at shankar.dutt@anu.edu.au.
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