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)) install.packages("BiocManager") BiocManager::install("scds", version = "3.10")
Or directly from github using
In the following
sce is a
SingleCellExperiment holding at least raw counts in an assay called
#- 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)
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