Work

Splatter: simulation of single-cell RNA sequencing data

Year: 2017

Type: article

Abstract: As single-cell RNA sequencing (scRNA-seq) technologies have rapidly developed, so have analysis methods. Many methods have been tested, developed, and validated using simulated datasets. Unfortunately, current simulations are often poorly documented, their similarity to real data is not demonstrated, or reproducible code is not available. Here, we present the Splatter Bioconductor package for simple, reproducible, and well-documented simulation of scRNA-seq data. Splatter provides an interface to multiple simulation methods including Splat, our own simulation, based on a gamma-Poisson distribution. Splat can simulate single populations of cells, populations with multiple cell types, or differentiation paths.

Source: Genome biology

DOI: 10.1186/s13059-017-1305-0

Authors: Luke Zappia, Belinda Phipson, Alicia Oshlack

Institutions: Royal Children's Hospital, The University of Melbourne, Murdoch Children's Research Institute

Language: English

Topic: Single-cell and spatial transcriptomics

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: gold

Estimated APC paid: $5,490

Funders: Australian Government, State Government of Victoria, Medical Research Council, National Health and Medical Research Council