# scds **s**ingle **c**ell **d**oublet **s**coring: 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)](https://doi.org/doi:10.18129/B9.bioc.SingleCellExperiment), so it should easily integrate into many ```R```/Bioconductor scRNA-seq analysis workflows. #### Installation You can install `scds` using [Bioconductor](https://bioconductor.org) (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) ``` #### Other doublet detection tools: * [DoubletCells](https://bioconductor.org/packages/release/workflows/vignettes/simpleSingleCell/inst/doc/work-6-doublet.html) as part of [SimpleSingleCell](https://bioconductor.org/packages/release/workflows/html/simpleSingleCell.html) * [DoubletDecon](https://github.com/EDePasquale/DoubletDecon) * [DoubletDetection](https://github.com/JonathanShor/DoubletDetection) * [DoubletFinder](https://github.com/chris-mcginnis-ucsf/DoubletFinder) * [Scrublet](https://github.com/AllonKleinLab/scrublet)