rust-bandnorm
Rust port of BandNorm (Shen, Zheng, Keleș 2022) — single-cell Hi-C scGAD scoring and band-normalisation for cell-type discovery and downstream embedding.
This is a separate package that re-implements the algorithm in Rust; it is not a fork of the upstream R tree. The original R implementation continues to be available at https://github.com/sshen82/BandNorm.
What it computes
Two functions, mirroring BandNorm/R/scGAD.R and BandNorm/R/bandnorm.R:
import bandnorm_rs as bn
# scGAD: gene × cell matrix from contact pairs.
gad = bn.scgad(hic_df, genes, resolution=10_000, depth_norm=True)
# BandNorm: per (chrom, diagonal, cell) depth-normalisation of contact counts.
norm_df = bn.bandnorm(hic_df)
Both are bit-equivalent (within f64 ε) to the R reference and faster by ~10-30× depending on the dataset.
Algorithm parity
tests/test_parity.py compares the Rust output against an R reference
generated via pure GenomicRanges (no GenomicInteractions dependency)
on the official BandNorm-shipped scGADExample.rda + mm9Annotations
data: 100 cells × ~1.3 M contact pairs × 10180 genes.
Tolerance: max |Rust − R| < 1e-10 on raw counts (integer-exact),
< 1e-6 on Z-scored GAD output.
Install
git clone https://github.com/omicverse/rust-bandnorm
cd rust-bandnorm
maturin develop --release
PyPI release coming soon (pip install bandnorm-rs).
Layout
rust-bandnorm/
├── pyproject.toml
├── rust/Cargo.toml
├── rust/src/lib.rs # ~250 LoC: gene index + scGAD + bandnorm
├── python/bandnorm_rs/ # Python wrapper
└── tests/
├── reference_scgad.R # R reference generator
└── test_parity.py # pytest parity vs R
License
MIT.
1 maintainer
Metadata
1 maintainer
Release files for bandnorm-rs 0.1.0
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| bandnorm_rs-0.1.0.tar.gz | 12.1 kB | With provenance | Details |
Built distributions (wheels)
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| bandnorm_rs-0.1.0-cp39-abi3-win_amd64.whl | CPython 3.9 | abi3 | Windows x86-64 | Details |
| bandnorm_rs-0.1.0-cp39-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl | CPython 3.9 | abi3 | Linux glibc 2.17+ x86-64 | Details |
| bandnorm_rs-0.1.0-cp39-abi3-manylinux_2_17_aarch64.manylinux2014_aarch64.whl | CPython 3.9 | abi3 | Linux glibc 2.17+ ARM64 | Details |
| bandnorm_rs-0.1.0-cp39-abi3-macosx_11_0_arm64.whl | CPython 3.9 | abi3 | macOS 11.0+ ARM64 | Details |
| bandnorm_rs-0.1.0-cp39-abi3-macosx_10_12_x86_64.whl | CPython 3.9 | abi3 | macOS 10.12+ x86-64 | Details |
Total release size: 1.5 MB
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