Presto - MattHuff/scRNASeq_011224 GitHub Wiki

Load Packages, Set Working Directory, and Load RDS

# Load Packages
library(Seurat)
library(dplyr)
library(ggplot2)
library(cowplot)
library(presto)

# Set Working Directory
setwd("~/Downloads/scRNASeq_011224/5_Seurat/")

# Optional - Load RDS
h5_seurat_no_dbl <- readRDS("outputs/5_filtered_integrated_norris.rds")
DefaultAssay(h5_seurat_no_dbl) <- "integrated"

Get Clusters

h5_seurat_no_dbl$seurat_clusters <- h5_seurat_no_dbl$integrated_snn_res.0.6

Run Presto

presto_markers <- wilcoxauc(h5_seurat_no_dbl, "seurat_clusters", seurat_assay = "SCT")

## Write markers to output file:
write.csv(presto_markers, file = "outputs/presto_markers_clusters.csv")

## Get Top 20 markers, write to output file:
top <- top_markers(presto_markers, n = 20)
write.csv(top, file = "outputs/top20_presto_markers_clusters.csv")

Save RDS file

saveRDS(h5_seurat_no_dbl, "outputs/6_clustered_integrated_norris.rds")