Benchmarking methods for detecting differential states between conditions from multi-subject single-cell RNA-seq data.

ABSTRACT: Single-cell RNA-sequencing (scRNA-seq) enables researchers to quantify transcriptomes of thousands of cells simultaneously and study transcriptomic changes between cells. scRNA-seq datasets increasingly include multisubject, multicondition experiments to investigate cell-type-specific differential states (DS) between conditions. This can be performed by first identifying the cell types in all the subjects and then by performing a DS analysis between the conditions within each cell type. Naïve single-cell DS analysis methods that treat cells statistically independent are subject to false positives in the presence of variation between biological replicates, an issue known as the pseudoreplicate bias. While several methods have already been introduced to carry out the statistical testing in m

SUBMITTER: Junttila S 

PROVIDER: S-EPMC9487674 | biostudies-literature | 2022 Sep

REPOSITORIES: biostudies-literature