DIEM
Remove debris-contaminated droplets from single-cell based data.
Installation
diem requires the following packages to be installed:
The diem package also makes use of the ggplot2 and scales packages
for plotting.
Currently, we only support installation of the diem R package
through devtools
library(devtools)
devtools::install_github("marcalva/diem")Usage
Check out the vignette for a thorough tutorial on using diem.
Shown below is a quick workflow for reading 10X data, filtering droplets using default parameters, and converting to a seurat object
library(diem)
library(Seurat)
counts <- read_10x("path/to/10x")
sce <- create_SCE(counts)
sce <- diem(sce)
seur <- convert_to_seurat(sce)