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.


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

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

Or directly from github using devtools:


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))

Other doublet detection tools:

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scds documentation built on Nov. 8, 2020, 7:01 p.m.