spacexr: spacexr: an R package for assigning cell types and cell type...
In dmcable/RCTD: SpatialeXpressionR: Cell type identification and cell type-specific differential expression in spatial transcriptomics
spacexr R Documentation
spacexr: an R package for assigning cell types and cell type specific differential expression to spatial transcriptomics data.
Running RCTD
To get started, create a SpatialRNA object (called puck here) for the
spatial transcriptomics data and a Reference object (called reference here) for the
scRNA-seq data. Then simply run RCTD as:
myRCTD <- create.RCTD(puck, reference)
myRCTD <- run.RCTD(myRCTD)
Running CSIDE
After running RCTD, create an explanatory variable ('explanatory.variable') representing a covariate hypothesized to explain gene expression.
Then, to detect cell type-specific differential expression, simply run CSIDE as:
myRCTD <- run.CSIDE.single(puck, explanatory.variable)
dmcable/RCTD documentation built on Feb. 24, 2024, 11:03 p.m.
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| spacexr | R Documentation |
spacexr: an R package for assigning cell types and cell type specific differential expression to spatial transcriptomics data.
Running RCTD
To get started, create a SpatialRNA object (called puck here) for the
spatial transcriptomics data and a Reference object (called reference here) for the
scRNA-seq data. Then simply run RCTD as:
myRCTD <- create.RCTD(puck, reference)
myRCTD <- run.RCTD(myRCTD)
Running CSIDE
After running RCTD, create an explanatory variable ('explanatory.variable') representing a covariate hypothesized to explain gene expression. Then, to detect cell type-specific differential expression, simply run CSIDE as:
myRCTD <- run.CSIDE.single(puck, explanatory.variable)
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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