tikhonov (Python)
Python bindings for tikhonov, a pure-Rust port of Harmony2 for single-cell data integration.
Install
pip install tikhonov
Quickstart (AnnData)
import tikhonov
import scanpy as sc
adata = sc.read_h5ad("my_data.h5ad")
# PCA already computed → obsm["X_pca"]
tikhonov.integrate(adata, key="sample", basis="X_pca", adjusted_basis="X_harmony")
# adata.obsm["X_harmony"] now holds the corrected embedding
Quickstart (arrays, harmonypy-compatible signature)
import numpy as np
import pandas as pd
import tikhonov
Z = np.random.randn(1000, 20) # (n_cells, n_PCs)
meta = pd.DataFrame({"sample": np.random.choice(["a", "b"], 1000)})
out = tikhonov.run_harmony(Z, meta, "sample", sigma=0.1, theta=2.0, max_iter=10)
print(out.Z_corr.shape) # (1000, 20)
print(out.converged, out.n_iter)
License
Apache-2.0.
1 maintainer
Metadata
1 maintainer
Release files for tikhonov 0.1.0
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Built distributions (wheels)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| tikhonov-0.1.0-cp310-abi3-win_amd64.whl | CPython 3.10 | abi3 | Windows x86-64 | Details |
| tikhonov-0.1.0-cp310-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl | CPython 3.10 | abi3 | Linux glibc 2.17+ x86-64 | Details |
| tikhonov-0.1.0-cp310-abi3-macosx_11_0_arm64.whl | CPython 3.10 | abi3 | macOS 11.0+ ARM64 | Details |
Total release size: 3.6 MB
Release files / tikhonov-0.1.0-cp310-abi3-win_amd64.whl
| Download URL | tikhonov-0.1.0-cp310-abi3-win_amd64.whl |
|---|---|
| Size | 721.0 kB |
| Tags | CPython 3.10 Windows x86-64 abi3 |
|
SHA-256 checksum How to use checksums |
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| Download URL | tikhonov-0.1.0-cp310-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl |
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| Size | 2.4 MB |
| Tags | CPython 3.10 Linux glibc 2.17+ x86-64 abi3 |
|
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| Download URL | tikhonov-0.1.0-cp310-abi3-macosx_11_0_arm64.whl |
|---|---|
| Size | 523.6 kB |
| Tags | CPython 3.10 abi3 macOS 11.0+ ARM64 |
|
SHA-256 checksum How to use checksums |
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| Uploaded via |
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