Cell-free DNA analysis toolkit
This is a Python package for easy and efficient cell-free DNA analysis.
All citations should reference to original 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
Create environment and pip install:
conda create -n cfdna python=3.11.3
conda activate cfdna
pip install cfdna
Dependencies can be installed by:
pip install -r requirements.txt
PyPI install, presuming you have all its requirements installed:
pip install cfdna
Usage
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 --genome hg19 --bin_size 100000
This will output a .png plot and seg file.
1 maintainer
Metadata
1 maintainer
Release files for cfdna 2.6.1
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| cfdna-2.6.1.tar.gz | 61.2 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| cfdna-2.6.1-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 133.0 kB
Release files / cfdna-2.6.1.tar.gz
| Download URL | cfdna-2.6.1.tar.gz |
|---|---|
| Size | 61.2 kB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
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Release files / cfdna-2.6.1-py3-none-any.whl
| Download URL | cfdna-2.6.1-py3-none-any.whl |
|---|---|
| Size | 71.9 kB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
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No |
| Uploaded via |
poetry/2.2.1 CPython/3.13.9 Darwin/25.6.0
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