README.md
In scds: In-Silico Annotation of Doublets for Single Cell RNA Sequencing Data

scds

single cell doublet scoring: In-silico doublet annotation for single cell RNA sequencing data

scds is an R package for computational doublet annotation of single cell RNA sequencing data. It interfaces with the S4 SingleCellExperiment class (see here), so it should easily integrate into many R/Bioconductor scRNA-seq analysis workflows.

Installation

You can install scds using Bioconductor (Devel Release 3.10) as follows:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("scds", version = "3.10")

Or directly from github using devtools:

devtools::install_github('kostkalab/scds',ref="master")

Quick Start

In the following sce is a SingleCellExperiment holding at least raw counts in an assay called counts.

#- Annotate doublet using co-expression based doublet scoring:
sce = cxds(sce)

#- Annotate doublet using binary classification based doublet scoring:
sce = bcds(sce)

#- Combine both annotations into a hybrid annotation
sce = cxds_bcds_hybrid(sce)

#- Doublet scores are now available via colData:
CD  = colData(sce)
head(cbind(CD$cxds_score,CD$bcds_score, CD$hybrid_score))
rm(CD)