R script for 10X SingleCell data analyzed by Seurat (include: QC、PCA、TSNE、UMAP、Cluster、FindAllMarkers、etc.)
Seurat_Single_Sample is used for analysing the single data from 10X cellranger. Seurat_multi_Sample is used for integrating the results from Seurat_Single_Sample.
Usage:
Rscript Seurat_Single_Sample.R 10X_matrix_dir output_dir Sample_name
Rscript Seurat_multi_Sample.R A.rds,B.rds,C.rds,D.rds output_dir
(All Parameters in the R scripts can be changed by user.)
R scripts for 10x SingleCelll data include CytoTRACE, slingshot,SCENIC,copycat inferCNV,GSVA, GSEA analysis and hierarchical clustering etc.
CytoTRACE_method is used to predict differentiation potential of cells
The method of slingshot is used to analysis pseudotim trajectory
SCNICIC_method is used to analysis to transcription factor activity in single cells
copycat_method is used for CNV analysis to discrimination between malignant and nonmaligant cells
inferCNV_method is another method to analysis CNV
GSVA_method is used for pathway activity
GSEA_method is used to analysis metabolism activity
hierarchical_cluster_method is used for hierarchical clustering
Usage:
Rscripts CytoTRACE_method.R 10x.seurat.rds outdir prefix
Rscripts slingshot_method.R 10x.seurat.rds outdir prefix
Rscripts SCENIC_method.R 10x.seurat.rds hg38_cistarget_db outdir prefix
Rscripts copycat_method.R 10x.seurat.rds outdir prefix
Rscripts inferCNV_method.R 10x.seurat.rds grch38.bed outdir prefix
Rscripts GSVA_method.R 10x.seurat.rds pathway.db outdir prefix
Rscripts GSEA_method.R 10x.seurat.rds metabolism.pathway.db outdir prefix
Rscripts hierarchical_cluster_method.R 10x.seurat.rds outdir prefix
Note: Before using this two R script, you need to install R(version >= 3.5) and some libraries(DoubletFinder、Seurat).
R: https://www.r-project.org/
BoubletFinder: https://github.com/chris-mcginnis-ucsf/DoubletFinder
Seurat: https://github.com/satijalab/seurat