spatialDWLS: cell type deconvolution of spatial spots

Estimate what fraction of each spot is made up of each cell type, given a mean-expression reference built from single-cell data.

• dwls() deconvolves an in-memory expression matrix.

• dwls_stream() does the same for a backend that reads spots in windows, so the expression never has to fit in memory at once.

• dwls_signature() builds the reference from a single-cell matrix.

References

Dong R, Yuan GC (2021). SpatialDWLS: accurate deconvolution of spatial transcriptomic data. Genome Biology 22, 145. doi:10.1186/s13059-021-02362-7

Tsoucas D, Dong R, Chen H, Zhu Q, Guo G, Yuan GC (2019). Accurate estimation of cell-type composition from gene expression data. Nature Communications 10, 2975. doi:10.1038/s41467-019-10802-z

See also

Useful links:

• https://drieslab.github.io/spatialDWLS/

• https://github.com/drieslab/spatialDWLS

• Report bugs at https://github.com/drieslab/spatialDWLS/issues

Author

Maintainer: Ruben Dries rubendries@gmail.com (ORCID)

Authors:

• Ruben Dries rubendries@gmail.com (ORCID)

• Rui Dong (original spatialDWLS implementation)

• Guo-Cheng Yuan guo-cheng.yuan@mssm.edu

Other contributors:

• Jiaji George Chen jiajic@bu.edu [contributor]