scDesign2: a transparent simulator that generates high-fidelity single-cell gene expression count data with gene correlations captured.
|
IF: 17.906
|
Cited by: 24
|

Abstract

A pressing challenge in single-cell transcriptomics is to benchmark experimental protocols and computational methods. A solution is to use computational simulators, but existing simulators cannot simultaneously achieve three goals: preserving genes, capturing gene correlations, and generating any number of cells with varying sequencing depths. To fill this gap, we propose scDesign2, a transparent simulator that achieves all three goals and generates high-fidelity synthetic data for multiple single-cell gene expression count-based technologies. In particular, scDesign2 is advantageous in its transparent use of probabilistic models and its ability to capture gene correlations via copulas.

Keywords

Omics
MERFISH
Seurat
Spatial Transcriptomics
pciSeq
Gene Expression
ISS

MeSH terms

Animals
Calibration
Cell Count
Cluster Analysis
Computer Simulation
Gene Expression Regulation
Genomics
Goblet Cells
Humans
Mice
RNA-Seq
Single-Cell Analysis
Software

Authors

Sun, Tianyi
Song, Dongyuan
Li, Wei Vivian
Li, Jingyi Jessica

Recommend literature





Similar data