Pre-release
This release is a pre-release and may not be stable for production use.
dnax — DNA models in JAX
[!WARNING] This is an experimental implementation.
dnax provides JAX-based implementation of models like BPNet, ChromBPNet, DragoNNFruit.
The code is heavily based on original implementations (chrombpnet, bpnet-lite)
however attempts to be more readable, accessible, and maintainable.
Installation
pip install dnax
# or
pip install git+https://github.com/gtca/dnax.git
Usage
Vanilla ChromBPNet:
from dnax.models.chrombpnet import ChromBPNet
bias = BPNet(n_filters=512, n_layers=8)
accessibility = BPNet(n_filters=512, n_layers=8)
model = ChromBPNet(bias, accessibility)
x = ... # (batch, 2114, 4) tensor (1-hot)
profile, counts = model(x)
For inference, you can load existing ChromBPNet models:
from dnax.io import load_chrombpnet_model
model = load_chrombpnet_model(bias_file, accessibility_file)
profile, counts = model(x)
Implementation
dnax currently uses flax and its NNX API.
1 maintainer
Metadata
1 maintainer
Release files for dnax 2024.0.0a1
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| dnax-2024.0.0a1.tar.gz | 14.5 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| dnax-2024.0.0a1-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 24.7 kB
Release files / dnax-2024.0.0a1.tar.gz
| Download URL | dnax-2024.0.0a1.tar.gz |
|---|---|
| Size | 14.5 kB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
ded2ce9e955c08eea88d3db19a61cac012a34e60e5aaf9b737fdb89315c01f81
|
|
BLAKE2b-256 checksum How to use checksums |
d4914bf39d3f7a8ea4883f5ec0e7ec887b6d58b4a6afd080934e7a5859a97235
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/5.1.1 CPython/3.11.9
|
Release files / dnax-2024.0.0a1-py3-none-any.whl
| Download URL | dnax-2024.0.0a1-py3-none-any.whl |
|---|---|
| Size | 10.2 kB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
b534b79d3bbc555604ec658d61383be12581a012c341b45a4a084ed6d64583ae
|
|
BLAKE2b-256 checksum How to use checksums |
07d654b4396d74b9fd1a568d06e4429e9ea60497c2dd9703887fc438f6448038
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/5.1.1 CPython/3.11.9
|
