inst/helpers/diffex.md
In whtns/seuratTools: Tools for Managing Seurat Objects
Differential expression
Differential expression can be used to identify genes which vary significantly between two populations of cells. Testing is executed via Seurat::FindMarkers and can be specified to use several methods including:
1. Student's t-test
2. Wilcoxon rank-sum test
3. Likelihood ratio test assuming an underlying negative binomial distribution
4. MAST: GLM-framework that treates cellular detection rate as a covariate (Finak et al, Genome Biology, 2015) (Installation instructions)
Comparison groups can be selected based on pre-computed cluster information or can be specified based on lasso-selection from a dimensionally reduced plot. Differential expression results for each method can be displayed in an associated table.
whtns/seuratTools documentation built on June 28, 2024, 8:30 p.m.
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Differential expression
Differential expression can be used to identify genes which vary significantly between two populations of cells. Testing is executed via Seurat::FindMarkers and can be specified to use several methods including:
1. Student's t-test
2. Wilcoxon rank-sum test
3. Likelihood ratio test assuming an underlying negative binomial distribution
4. MAST: GLM-framework that treates cellular detection rate as a covariate (Finak et al, Genome Biology, 2015) (Installation instructions)
Comparison groups can be selected based on pre-computed cluster information or can be specified based on lasso-selection from a dimensionally reduced plot. Differential expression results for each method can be displayed in an associated table.
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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