scGSVA
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scGSVA: Perform GSVA for single cell RNA seq
scGSVA: GSVA for single-cell RNA seq analysis. Now support UCell scoring
scGSVA
![Code Size:](https://img.shields.io/github/languages/code-size/guokai8/scGSVA)
Description
scGSVA provides wrap functions to do GSVA analysis for single-cell data. And scGSVA includes functions to build annotation for almost all species. scGSVA also provides functions to generate figures based on the GSVA results.
scGSVA provides functions to generate annotation data which can be used in the analysis.
Fixed some issues since there was a bug due to the KEGG annotation changed these days.
Add batch calculation when the cell population is huge.
Add UCell function within the scgsva function. Users need to install UCell by using BiocManager::install("UCell").
Add spatialFeaturePlot function for spatial transcriptomics.
Installation
library(devtools)
install_github("guokai8/scGSVA")
Examples
set.seed(123)
library(scGSVA)
data(pbmcs)
hsko<-buildAnnot(species="human",keytype="SYMBOL",anntype="KEGG")
res<-scgsva(pbmcs,hsko,method="ssgsea") ## or use UCell
vlnPlot(res,features="Wnt.signaling.pathway",group_by="groups") ## split.plot = TRUE and split.by
![](https://github.com/guokai8/scGSVA/raw/main/vln.jpg)
dotPlot(res,features="Wnt.signaling.pathway",group_by="groups")
![](https://github.com/guokai8/scGSVA/raw/main/dot.png)
ridgePlot(res,features="Wnt.signaling.pathway",group_by="groups")
![](https://github.com/guokai8/scGSVA/raw/main/ridge.jpg)
featurePlot(res,features="Wnt.signaling.pathway", reduction="tsne", group_by="groups")
![](https://github.com/guokai8/scGSVA/raw/main/feature.png)
Heatmap(res,group_by="groups")
![](https://github.com/guokai8/scGSVA/raw/main/heat.jpg)
## Find significant pathways across groups
findPathway(res,group = "groups")
sigPathway(res, group = "groups")
## Extract specific pathways with expression value
genes(res, features = "Wnt.signaling.pathway")
Note
The scGSVA package uses the GSVA package to do the GSVA analysis for the single cell data. The package is still under development.
Contact information
For any questions please contact [email protected] or https://github.com/guokai8/scGSVA/issues
Recently update
Try to do multiple p-value corrections within group-wise other than overall.