empty_drop_citeseq_mtx {dsb}

small example CITE-seq protein dataset for 87 surface protein in 8005 empty droplets

Description

A matrix of empty background droplet counts for surface proteins measured with CITE-seq antibodies. This data is used for example scripts in the dsb package. Raw data was processed with CITE-seq-Count.

Usage

empty_drop_citeseq_mtx

Format

An R matrix, rows: 87 proteins, columns: 8005 empty droplets.

empty_drop_citeseq_mtx

R matrix of empty / background droplets from a CITE-seq experiment. Negative drops were called on cell hashing data with Seurat's HTODemux function and cross referencing mRNA in droplets against patient genotypes with Demuxlet. Ambiguous drops, and with less than 80 unique mRNA were removed. This is used for robust estimation of the background distribution of each protein

References

Kotliarov et. al. 2020 Nat. Medicine