Python extension of CNVnator
Project description
CNVpytor - a python extension of CNVnator
CNVpytor is a Python package and command line tool for CNV/CNA analysis from depth-of-coverage by mapped reads developed in Abyzov Lab, Mayo Clinic.
NEW: CNVpytor release ver 1.0 is available to install!
Learn how to use CNVpytor in 10 minutes
- Geting started with command line interface
- Jupyter notebook: How to use CNVpytor from Python
- Google Colab: With CEPH trio example dataset
Gallery
| Manhattan plot (see example) | Circular plot (see example) |
| Region plot (see example) | Compare regions (see example) |
Dependencies
- requests>=2.0
- gnureadline
- pathlib>=1.0
- pysam>=0.15
- numpy>=1.16
- scipy>=1.1
- matplotlib>=2.2
- h5py>=2.9
Optional:
- pyBigWig - for JBrowse export functionality
- ROOT - for CNVnator root import/export functionality
- seaborn - for additional plotting styles
Install
> pip install cnvpytor
> cnvpytor -download
Using
Check CNVpytor github page.
License
Released under MIT licence.
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| Filename, size | File type | Python version | Upload date | Hashes |
|---|---|---|---|---|
| Filename, size CNVpytor-1.0.tar.gz (148.4 kB) | File type Source | Python version None | Upload date | Hashes View |