SpotClean-package: SpotClean: a computational method to adjust for spot swapping...
In zijianni/SpotClean: SpotClean adjusts for spot swapping in spatial transcriptomics data
SpotClean-package R 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 Nov. 15, 2023, 12:53 a.m.
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| SpotClean-package | R 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:
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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