PyNanoLab is an all-in-one GUI software for data analysis and visualization, expecially for nanopore analysis.
In the version 3.X, binary installer (*.exe) is not provided anymore owing to the complex workflow and lost feature and performance.
We recommend you use the pip install to obtain all the advanced features.
Firstly, you should have already installed the python or conda virtual environment in your system.
Miniconda is recommended. And you should add the conda to your system environment variable.
In windows, you also need to install a terminal. git-windows or windows-terminal is recommended.
PyNanoLab depend on th PySide6 to create its GUI. And it's not compatible with the other PyQt package. So we highly recommend to install pynanolab to a new python virtual environment.
use following command in a terminal:
conda create -n pnl python=3.13.2
source activate
conda activate pnl # activate the pnl environment.
conda install numpy # optional, install the numpy-MKL to speed up the software.Then, you should install Pytorch on this environment (Any version, you should select a version, GPU verison is more better).
For example:
# CPU 版本
pip install torch torchvision torchaudio
# 或者自行安装GPU版本
pip3 install torch torchvision torchaudio --index-url https://download.pytorch.org/whl/cu128! warning: at windows, you should install hdbscan by manually compiling. For example using conda
conda install hdbscan -c conda-forgeIf using pip, you should have c/c++ compiler on your system.
Now, you have created a new python virtual environment and activated it. The name is pnl, and you can change the name to anything you want, and the python version is specified to >=3.11. (We recommend >=3.13.x)
Then, you can directly install as general python packages.
pip install pynanolab Use the above command, the pynanolab will be installed automaticly. And a entry fille will be created in the Scripts folder of the "pnl" virtual environment. In windows is named "pynanolab.exe" and "pynanolab" in Linux and MacOSX.
Then, you can directily conduct the following command to open it in a terminal with pnl virtual environment activated.
pynanolabIf you want to create a shortcut or a desktop entry. Use the following command:
pnl-shortcut
If you use the pip installtion. You can upgrade the packages manually using the following command:
pip install --upgrade pynanolab
- Extract signal automaticall
- Multiple File management
- Raw data denoise and filter
- Data filter and calculate with pandas
- iPython integration
- Manage your data like the excel
- Visualize data with matplotlib
- Interactive setup Figure
- Rebuild data and fig from project file.
- Curves fitting with lmfit
- Multiple build-in models
- Interactive fitting
- Clustering of with scikit-learn
- Interactive parameter setting
- Real-time visualization
- Custom and Auto signal analysis
- Time-Frequency spectral analysis
- Signal batch processing