SoupX removes ambient RNA contamination from droplet-based single-cell RNA sequencing data

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

(2020) Haynes Heaton et al.   NATURE METHODS

SoupX removes ambient RNA contamination from droplet-based single-cell RNA sequencing data

(2020) Matthew D Young et al.   GigaScience

Scrublet: Computational Identification of Cell Doublets in Single-Cell Transcriptomic Data

(2019) Samuel L. Wolock et al.   Cell Systems

Decoding human fetal liver haematopoiesis

(2019) Dorin-Mirel Popescu et al.   NATURE

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

(2018) Laleh Haghverdi et al.   NATURE BIOTECHNOLOGY

Integrating single-cell transcriptomic data across different conditions, technologies, and species

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

Single-cell RNA-seq of rheumatoid arthritis synovial tissue using low-cost microfluidic instrumentation

(2018) William Stephenson et al.   Nature Communications

Single cell RNA sequencing of stem cell-derived retinal ganglion cells

(2018) Maciej Daniszewski et al.   Scientific Data

Single-cell transcriptomes from human kidneys reveal the cellular identity of renal tumors

(2018) Matthew D. Young et al.   SCIENCE

The Human Cell Atlas: from vision to reality

(2017) Orit Rozenblatt-Rosen et al.   NATURE

Power analysis of single-cell RNA-sequencing experiments

(2017) Valentine Svensson et al.   NATURE METHODS

Differentiation dynamics of mammary epithelial cells revealed by single-cell RNA sequencing

(2017) Karsten Bach et al.   Nature Communications

Massively parallel digital transcriptional profiling of single cells

(2017) Grace X. Y. Zheng et al.   Nature Communications

Comprehensive single-cell transcriptome analysis reveals heterogeneity in endometrioid adenocarcinoma tissues

(2017) Shinichi Hashimoto et al.   Scientific Reports

Single-cell RNA sequencing identifies distinct mouse medial ganglionic eminence cell types

(2017) Ying-Jiun J. Chen et al.   Scientific Reports

The Human Cell Atlas

(2017) Aviv Regev et al.   eLife

Single-cell barcoding and sequencing using droplet microfluidics

(2016) Rapolas Zilionis et al.   Nature Protocols

Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets

(2015) Evan Z. Macosko et al.   CELL

Spatial reconstruction of single-cell gene expression data

(2015) Rahul Satija et al.   NATURE BIOTECHNOLOGY