scrnaseq-mouse: scRNA-seq, mouse dataset results

In stephaniehicks/benchmarkfdrData2019: Data and Benchmarking Results from Korthauer and Kimes et al. (2019)

scRNA-seq, mouse dataset results

Description

Results for case study on single-cell RNA-seq differential expression analysis using data from mouse cells at NF-kappa-beta activation as described in Korthauer and Kimes et al. (2019). Differential expression was testing using either the MAST package, scDD package, or Wilcoxon rank-sum test.

Arguments

metadata

logical whether to load metadata (TRUE) or full resource (FALSE). (default = FALSE)

Details

Results for this case study include:

• mouse-benchmark-mast-det: testing with MAST, using detection rate as covariate.

• mouse-benchmark-mast-mean: testing with MAST, using mean counts as covariate.

• mouse-benchmark-mast-uninf: testing with MAST, using uninformative covariate.

• mouse-benchmark-scdd-det: testing with scDD, using detection rate as covariate.

• mouse-benchmark-scdd-mean: testing with scDD, using mean counts as covariate.

• mouse-benchmark-scdd-uninf: testing with scDD, using uninformative covariate.

• mouse-benchmark-wilcox-det: testing with Wilcoxon rank-sum, using detection rate as covariate.

• mouse-benchmark-wilcox-mean: testing with Wilcoxon rank-sum, using mean counts as covariate.

• mouse-benchmark-wilcox-uninf: testing with Wilcoxon rank-sum, using uninformative covariate.

See Also

scrnaseq-human

Examples

`mouse-benchmark-mast-det`(metadata = TRUE)

## Not run: 
`mouse-benchmark-mast-det`()
`mouse-benchmark-mast-mean`()
`mouse-benchmark-mast-uninf`()
`mouse-benchmark-scdd-det`()
`mouse-benchmark-scdd-mean`()
`mouse-benchmark-scdd-uninf`()
`mouse-benchmark-wilcox-det`()
`mouse-benchmark-wilcox-mean`()
`mouse-benchmark-wilcox-uninf`()

## End(Not run)

stephaniehicks/benchmarkfdrData2019 documentation built on April 13, 2025, 9:02 p.m.