singleCellHaystack 0.0.3

An implementation of [singleCellHaystack](https://github.com/alexisvdb/singleCellHaystack) in python.

singleCellHaystack

This repository contains a python implementation of singleCellHaystack.

Installation

You can install singleCellHaystack from pypi:

pip install singleCellHaystack

Example

import scanpy as sc
import singleCellHaystack as hs

adata = sc.read_h5ad("data.h5ad")

res = hs.haystack(adata)

References

• Our manuscript describing the updated, more generally applicable version of singleCellHaystack inclusing this python implementation is available on bioRxiv.

• Our manuscript describing the original implementation of singleCellHaystack for R (version 0.3.4) was published in Nature Communications.

If you use singleCellHaystack in your research please cite our work using:

Vandenbon A, Diez D (2020). “A clustering-independent method for finding differentially expressed genes in single-cell transcriptome data.” Nature Communications, 11(1), 4318. doi:10.1038/s41467-020-17900-3.