This package performs principal component analysis (PCA) on the scaled Seurat object.
The package can be installed using
devtools::install_github("BTIP/pca-seurat")
The output of this function would be 2D and 3D plots.
pca_seurat("after_scaling.rds")
The standard scRNAseq processing workflow with the R package Seurat consists of seven (7) steps. This package is the sixth (6th) step of the workflow.
The following are the repositories of the packages for every step of the pipeline:
- QC and filtering: qualitycontrolseurat package
- Normalization: qualitycontrolseurat package
- Identification of highly variable features: selectionscalingseurat package
- Scaling: selectionscalingseurat package
- Linear Dimensionality Reduction (PCA): pcaseurat package
- Clustering: nonlinearreduction package
- Non-linear dimensionality reduction (t-SNE and UMAP): nonlinearreduction package
An overview of the pipeline and its outputs can be observed below:
