DoubletFinder: doublet detection in single-cell RNA sequencing data using artificial nearest neighbors

CS McGinnis, LM Murrow, ZJ Gartner - Cell systems, 2019 - cell.com
Single-cell RNA sequencing (scRNA-seq) data are commonly affected by technical artifacts
known as" doublets," which limit cell throughput and lead to spurious biological conclusions …

scds: computational annotation of doublets in single-cell RNA sequencing data

AS Bais, D Kostka - Bioinformatics, 2020 - academic.oup.com
Motivation Single-cell RNA sequencing (scRNA-seq) technologies enable the study of
transcriptional heterogeneity at the resolution of individual cells and have an increasing …

Benchmarking computational doublet-detection methods for single-cell RNA sequencing data

NM Xi, JJ Li - Cell systems, 2021 - cell.com
In single-cell RNA sequencing (scRNA-seq), doublets form when two cells are encapsulated
into one reaction volume. The existence of doublets, which appear to be—but are not—real …

[HTML][HTML] DoubletDecon: deconvoluting doublets from single-cell RNA-sequencing data

EAK DePasquale, DJ Schnell, PJ Van Camp… - Cell reports, 2019 - cell.com
Methods for single-cell RNA sequencing (scRNA-seq) have greatly advanced in recent
years. While droplet-and well-based methods have increased the capture frequency of cells …

Solo: doublet identification in single-cell RNA-seq via semi-supervised deep learning

NJ Bernstein, NL Fong, I Lam, MA Roy… - Cell systems, 2020 - cell.com
Single-cell RNA sequencing (scRNA-seq) measurements of gene expression enable an
unprecedented high-resolution view into cellular state. However, current methods often …

Scrublet: computational identification of cell doublets in single-cell transcriptomic data

SL Wolock, R Lopez, AM Klein - Cell systems, 2019 - cell.com
Single-cell RNA-sequencing has become a widely used, powerful approach for studying cell
populations. However, these methods often generate multiplet artifacts, where two or more …

Valid post-clustering differential analysis for single-cell RNA-Seq

JM Zhang, GM Kamath, NT David - Cell systems, 2019 - cell.com
Single-cell computational pipelines involve two critical steps: organizing cells (clustering)
and identifying the markers driving this organization (differential expression analysis). State …

Souporcell: robust clustering of single-cell RNA-seq data by genotype without reference genotypes

H Heaton, AM Talman, A Knights, M Imaz, DJ Gaffney… - Nature …, 2020 - nature.com
Methods to deconvolve single-cell RNA-sequencing (scRNA-seq) data are necessary for
samples containing a mixture of genotypes, whether they are natural or experimentally …

Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors

L Haghverdi, ATL Lun, MD Morgan, JC Marioni - Nature biotechnology, 2018 - nature.com
Large-scale single-cell RNA sequencing (scRNA-seq) data sets that are produced in
different laboratories and at different times contain batch effects that may compromise the …

GMM-Demux: sample demultiplexing, multiplet detection, experiment planning, and novel cell-type verification in single cell sequencing

H Xin, Q Lian, Y Jiang, J Luo, X Wang, C Erb, Z Xu… - Genome biology, 2020 - Springer
Identifying and removing multiplets are essential to improving the scalability and the
reliability of single cell RNA sequencing (scRNA-seq). Multiplets create artificial cell types in …