SpotClean-package: SpotClean: a computational method to adjust for spot swapping...

SpotClean-packageR Documentation

SpotClean: a computational method to adjust for spot swapping in spatial transcriptomics data

Description

SpotClean is a computational method to adjust for spot swapping in spatial transcriptomics data. Recent spatial transcriptomics experiments utilize slides containing thousands of spots with spot-specific barcodes that bind mRNA. Ideally, unique molecular identifiers at a spot measure spot-specific expression, but this is often not the case due to bleed from nearby spots, an artifact we refer to as spot swapping. SpotClean is able to estimate the contamination rate in observed data and decontaminate the spot swapping effect, thus increase the sensitivity and precision of downstream analyses.

Details

To learn more about SpotClean, see the vignette using browseVignettes(package = "SpotClean").

Author(s)

Maintainer: Zijian Ni zni25@wisc.edu (ORCID)

Other contributors:

  • Christina Kendziorski [contributor]

See Also

Useful links:


zijianni/SpotClean documentation built on June 12, 2024, 1:58 a.m.