PyPI page
Author:
Mahdi Shafiei
License:
MIT License
Copyright (c) 2026 Mahdi Shafiei
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated docu...
Summary:
End-to-end differentiable bioinformatics for JAX/Flax NNX: alignment, mapping, assembly, variant calling, RNA-seq, single-cell, epigenomics, CRISPR, metabolomics, multi-omics, protein and RNA structure, molecular dynamics and drug-discovery operators composed into trainable pipelines on datarax, artifex, opifex and calibrax
Latest version:
0.1.9
Required dependencies:
anndata
|
avitai-artifex
|
beartype
|
biopython
|
calibrax
|
chex
|
datarax
|
flax
|
h5py
|
jax
|
jax-md
|
jaxtyping
|
numpy
|
opifex
|
optax
|
scipy
|
substrax
Optional dependencies:
bandit
|
beartype
|
build
|
coverage
|
datasets
|
deepchem
|
flake8
|
flake8-functions-names
|
griffe
|
import-linter
|
interrogate
|
ipykernel
|
jax
|
jax-metal
|
lineax
|
matplotlib
|
mkdocs
|
mkdocs-include-exclude-files
|
mkdocs-material
|
mkdocstrings
|
mkdocstrings-python
|
optimistix
|
ott-jax
|
pandas
|
pyfaidx
|
pylint
|
pymdown-extensions
|
pynndescent
|
pyright
|
pysam
|
pytest
|
pytest-asyncio
|
pytest-benchmark
|
pytest-cov
|
pytest-env
|
pytest-json-report
|
pytest-randomly
|
pytest-timeout
|
pytest-xdist
|
python-dotenv
|
pyyaml
|
radon
|
rdkit
|
ruff
|
scib-metrics
|
shellcheck-py
|
squidpy
|
tabulate
|
torch
|
wemake-python-styleguide
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