Crate infercnasc 

Copy number alteration (CNA) inference from single-cell RNA-seq data.

Overview

This crate provides a Rust-native pipeline for detecting chromosomal copy number gains and losses from scRNA-seq expression matrices. The three core functions form a sequential pipeline:

1. smooth_expression: applies a chromosome-aware sliding-window mean to reduce per-gene noise.
2. find_cnas: flags cells with z-scores above or below a threshold as gains or losses for each gene.
3. assign_cnas_to_cells: merges consecutive flagged genes on the same chromosome into CnaRecord regions using a run-length scan.

Example

use ndarray::array;
use infercnasc::{smooth_expression, find_cnas, assign_cnas_to_cells};

let expression = array![[1.0_f64, 2.0, 3.0], [4.0, 5.0, 6.0]];
let chroms = vec!["1", "1", "1"];

let smoothed = smooth_expression(&expression, &chroms, 3).unwrap();
let (gains, losses) = find_cnas(&smoothed, 1.5);
let records = assign_cnas_to_cells(
    &gains, &losses,
    &chroms,
    &[0, 1000, 2000],
    &[999, 1999, 2999],
    &["BRCA1", "TP53", "MYC"],
    2,
);

Errors

smooth_expression returns InferError::EmptyMatrix if the expression matrix has zero rows or columns, and InferError::ShapeMismatch if the length of chroms does not match the number of gene columns.

find_cnas and assign_cnas_to_cells are infallible.

Python bindings

The optional python feature exposes this pipeline via PyO3. Install the Python package with pip install infercnasc rather than enabling this feature directly.

Re-exports

pub use error::InferError;

pub use smooth::smooth_expression;

pub use cna::find_cnas;

pub use assign::assign_cnas_to_cells;

pub use assign::CnaRecord;

Modules

assign

cna

error

smooth