Splatter: simulation of single-cell RNA sequencing data. 2017

Luke Zappia, and Belinda Phipson, and Alicia Oshlack
Murdoch Childrens Research Institute, Royal Children's Hospital, 50 Flemington Rd, Parkville, VIC, 3052, Australia.

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.

UI MeSH Term Description Entries
D008957 Models, Genetic Theoretical representations that simulate the behavior or activity of genetic processes or phenomena. They include the use of mathematical equations, computers, and other electronic equipment. Genetic Models,Genetic Model,Model, Genetic
D003198 Computer Simulation Computer-based representation of physical systems and phenomena such as chemical processes. Computational Modeling,Computational Modelling,Computer Models,In silico Modeling,In silico Models,In silico Simulation,Models, Computer,Computerized Models,Computer Model,Computer Simulations,Computerized Model,In silico Model,Model, Computer,Model, Computerized,Model, In silico,Modeling, Computational,Modeling, In silico,Modelling, Computational,Simulation, Computer,Simulation, In silico,Simulations, Computer
D006801 Humans Members of the species Homo sapiens. Homo sapiens,Man (Taxonomy),Human,Man, Modern,Modern Man
D000818 Animals Unicellular or multicellular, heterotrophic organisms, that have sensation and the power of voluntary movement. Under the older five kingdom paradigm, Animalia was one of the kingdoms. Under the modern three domain model, Animalia represents one of the many groups in the domain EUKARYOTA. Animal,Metazoa,Animalia
D012984 Software Sequential operating programs and data which instruct the functioning of a digital computer. Computer Programs,Computer Software,Open Source Software,Software Engineering,Software Tools,Computer Applications Software,Computer Programs and Programming,Computer Software Applications,Application, Computer Software,Applications Software, Computer,Applications Softwares, Computer,Applications, Computer Software,Computer Applications Softwares,Computer Program,Computer Software Application,Engineering, Software,Open Source Softwares,Program, Computer,Programs, Computer,Software Application, Computer,Software Applications, Computer,Software Tool,Software, Computer,Software, Computer Applications,Software, Open Source,Softwares, Computer Applications,Softwares, Open Source,Source Software, Open,Source Softwares, Open,Tool, Software,Tools, Software
D015203 Reproducibility of Results The statistical reproducibility of measurements (often in a clinical context), including the testing of instrumentation or techniques to obtain reproducible results. The concept includes reproducibility of physiological measurements, which may be used to develop rules to assess probability or prognosis, or response to a stimulus; reproducibility of occurrence of a condition; and reproducibility of experimental results. Reliability and Validity,Reliability of Result,Reproducibility Of Result,Reproducibility of Finding,Validity of Result,Validity of Results,Face Validity,Reliability (Epidemiology),Reliability of Results,Reproducibility of Findings,Test-Retest Reliability,Validity (Epidemiology),Finding Reproducibilities,Finding Reproducibility,Of Result, Reproducibility,Of Results, Reproducibility,Reliabilities, Test-Retest,Reliability, Test-Retest,Result Reliabilities,Result Reliability,Result Validities,Result Validity,Result, Reproducibility Of,Results, Reproducibility Of,Test Retest Reliability,Validity and Reliability,Validity, Face
D016000 Cluster Analysis A set of statistical methods used to group variables or observations into strongly inter-related subgroups. In epidemiology, it may be used to analyze a closely grouped series of events or cases of disease or other health-related phenomenon with well-defined distribution patterns in relation to time or place or both. Clustering,Analyses, Cluster,Analysis, Cluster,Cluster Analyses,Clusterings
D017423 Sequence Analysis, RNA A multistage process that includes cloning, physical mapping, subcloning, sequencing, and information analysis of an RNA SEQUENCE. RNA Sequence Analysis,Sequence Determination, RNA,Analysis, RNA Sequence,Determination, RNA Sequence,Determinations, RNA Sequence,RNA Sequence Determination,RNA Sequence Determinations,RNA Sequencing,Sequence Determinations, RNA,Analyses, RNA Sequence,RNA Sequence Analyses,Sequence Analyses, RNA,Sequencing, RNA
D059010 Single-Cell Analysis Assaying the products of or monitoring various biochemical processes and reactions in an individual cell. Analyses, Single-Cell,Analysis, Single-Cell,Single Cell Analysis,Single-Cell Analyses
D066264 Datasets as Topic Subject matter related to the curation of data from research projects, stored permanently in a formalized manner suitable for communication, interpretation, or processing. Dataset as Topic,Data Sets as Topic

Related Publications

Luke Zappia, and Belinda Phipson, and Alicia Oshlack
May 2020, Bioinformatics (Oxford, England),
Luke Zappia, and Belinda Phipson, and Alicia Oshlack
November 2021, Nature communications,
Luke Zappia, and Belinda Phipson, and Alicia Oshlack
May 2022, Nucleic acids research,
Luke Zappia, and Belinda Phipson, and Alicia Oshlack
February 2023, Biochemistry. Biokhimiia,
Luke Zappia, and Belinda Phipson, and Alicia Oshlack
January 2021, Computational and structural biotechnology journal,
Luke Zappia, and Belinda Phipson, and Alicia Oshlack
November 2019, Human molecular genetics,
Luke Zappia, and Belinda Phipson, and Alicia Oshlack
September 2020, Briefings in bioinformatics,
Luke Zappia, and Belinda Phipson, and Alicia Oshlack
January 2023, Briefings in bioinformatics,
Luke Zappia, and Belinda Phipson, and Alicia Oshlack
June 2019, Nucleic acids research,
Luke Zappia, and Belinda Phipson, and Alicia Oshlack
November 2019, Cell reports,
Copied contents to your clipboard!