inst/rmarkdown/Rscripts/singlecell/markers_seurat.R

In hbc/hbcABC: Rmarkdown templates for bioinformatic analysis

# single cell find markers with seurat

library(Seurat)
library(tidyverse)
data_dir = "data"
set.seed(1454944673L)
# seurat_object = "seurat_tsne.rds"
# prefix = "xx"
seurat = readRDS(file = file.path(data_dir, seurat_object))
markers = FindAllMarkers(object = seurat, only.pos = TRUE, min.pct = 0.25,
                         thresh.use = 0.25)
saveRDS(markers, file.path(data_dir, paste0(prefix ,"_markers.rds")))
#rsync you data if you work in the cluster and local computer for the same data.