Metadata-Version: 2.1
Name: cfdna
Version: 1.0.3
Summary: Python package for fragment manipulation for cfDNA
Home-page: https://github.com/kylessmtih/cfdna
Author: Kyle S. Smith
Author-email: kyle.smith@stjude.org
License: GPL2
Description: # Cell-free DNA analysis toolkit
        
        [![Build Status](https://travis-ci.org/kylessmith/cfdna.svg?branch=master)](https://travis-ci.org/kylessmith/cfdna) [![PyPI version](https://badge.fury.io/py/cfdna.svg)](https://badge.fury.io/py/cfdna)
        
        This is a Python package for easy and efficient cell-free
        DNA analysis.
        
        All citations should reference to [original paper][paper].
        
        
        ## Install
        
        If you dont already have numpy and scipy installed, it is best to download
        `Anaconda`, a python distribution that has them included.  
        ```
            https://continuum.io/downloads
        ```
        
        Dependencies can be installed by:
        
        ```
            pip install -r requirements.txt
        ```
        
        PyPI install, presuming you have all its requirements installed:
        ```
            pip install cfdna
        ```
        
        ## Usage
        
        ```python
        import cfdna as cf
        import numpy as np
        
        # Create data
        cfdata = cf.cfDNA()
        frags = cf.io.readBAM("test.bam")
        
        # Call CNVs
        cf.proc.call_cnv_pipline(cfdata, frags)
        
        # Plot CNVs
        cf.pl.plot_cnv(cfdata, "test.bam")
        ```
        
        Run from the commadline:
        
        ```
            python -m cfdna callCNVs --bam test.bam --segs
        ```
        
        This will output a .png plot and seg file.
        
        [paper]: https://www.cell.com/cancer-cell/pdfExtended/S1535-6108(21)00501-8
Keywords: next generation sequencing fragment cfDNA cell free DNA
Platform: Linux
Classifier: Development Status :: 4 - Beta
Classifier: Environment :: Console
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: Operating System :: POSIX :: Linux
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.4
Classifier: Topic :: Scientific/Engineering
Classifier: Topic :: Scientific/Engineering :: Mathematics
Classifier: Topic :: Software Development :: Libraries
Classifier: Topic :: Software Development :: Libraries :: Python Modules
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Provides: cfdna
Description-Content-Type: text/markdown
