README.md

In diem: Debris-Containing Droplet Identification using EM

DIEM

Remove debris-contaminated droplets from single-cell based data.

Installation

diem requires the following packages to be installed:

• Matrix
• dbscan
• igraph

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)

diem documentation built on Nov. 16, 2019, 1:08 a.m.