basic_workflow: Basic Workflow
In scRNAstat: A Pipeline to Process Single Cell RNAseq Data
Description
Usage
Arguments
Value
Examples
View source: R/basic_workflow.R
Description
the workflow from Seurat, including: 'NormalizeData','FindVariableFeatures','ScaleData',
'RunPCA','RunTSNE','RunUMAP','FindNeighbors','FindClusters(sce, resolution = seq(0.1,1,by=0.1))'
we use 'clustree' to check the different resolution for 'FindClusters'.
Usage
1
basic_workflow(sce, dir = ".")
Arguments
sce
An object of class Seurat
dir
the path for saving the figures by 'DotPlot' with known famous markers.
Value
list(p1,p2,p3,sce), the last one in the new sce with PCA,tSNE,UMAP information.
Examples
1
2
3
4
## Not run:
basic_workflow(AJ064_small_sce,dir=tempdir())
## End(Not run)
scRNAstat documentation built on Sept. 22, 2021, 9:07 a.m.
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Description Usage Arguments Value Examples
View source: R/basic_workflow.R
Description
the workflow from Seurat, including: 'NormalizeData','FindVariableFeatures','ScaleData', 'RunPCA','RunTSNE','RunUMAP','FindNeighbors','FindClusters(sce, resolution = seq(0.1,1,by=0.1))' we use 'clustree' to check the different resolution for 'FindClusters'.
Usage
1 | basic_workflow(sce, dir = ".")
|
Arguments
sce |
An object of class Seurat |
dir |
the path for saving the figures by 'DotPlot' with known famous markers. |
Value
list(p1,p2,p3,sce), the last one in the new sce with PCA,tSNE,UMAP information.
Examples
1 2 3 4 | ## Not run:
basic_workflow(AJ064_small_sce,dir=tempdir())
## End(Not run)
|
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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