Improve Research Reproducibility A Bio-protocol resource
bpdetail_icon_lock
Preprint

Cell cluster annotation, trajectory inference, and signature enrichment

EL Ekaterini Maria Lyras
AM Alexander Mildner

Last updated date: Apr 5, 2023 Views: 289 Forks: 0

original An abbreviated version of this protocol was published in eLife
Tongue immune compartment analysis reveals spatial macrophage heterogeneity
download pdf Download PDF
ask Ask a question
cite How to cite
nfavorite Favorite

GSVA was performed according to the published protocol (https://bioconductor.org/packages/devel/bioc/vignettes/GSVA/inst/doc/GSVA.html). 

 

library("Seurat")
library("GSVA")

# load your seurat object and the signature genes you are interested in, here: "your.seurat.object" and "signature.genes.1"

signature.genes.1<-c("Adam19", "Amica1", "Ap1s3", "Ass1", "Bcl11a", "Btla", "Ccr7", "Flt3", "Gpr114",
          "Gpr132", "Gpr68", "Gpr82", "H2-Eb2", "Hmgn3", "Kit", "Klri1", "Kmo", "P2ry10", "Pvrl1",
          "Rab30", "Septin6", "Slamf7", "Traf1", "Zbtb46")


gs <- list(sig1=signature.genes.1)
Y<-GetAssayData(object=your.seurat.object, assay = "RNA", slot="data")
gsva.es <- gsva(Y, gs, verbose=FALSE)
your.seurat.object[["sig1"]]<-gsva.es["sig1",]
FeaturePlot(your.seurat.object, "sig1", cols=c("blue", "lightgrey", "red") )
 

Copyright: Content may be subjected to copyright.
How to cite：
Readers should cite both the Bio-protocol preprint and the original research article where this protocol was used:
  1. Lyras, E and Mildner, A(2023). Cell cluster annotation, trajectory inference, and signature enrichment. Bio-protocol Preprint. bio-protocol.org/prep2192.
  2. Tongue immune compartment analysis reveals spatial macrophage heterogeneity. eLife. DOI: 10.7554/eLife.77490

Do you have any questions about this protocol?

Post your question to gather feedback from the community. We will also invite the authors of this article to respond.

0/150

tip Tips for asking effective questions

+ Description

Write a detailed description. Include all information that will help others answer your question including experimental processes, conditions, and relevant images.

post Post a Question
0 Q&A
This protocol preprint was submitted via the "Request a Protocol" track.