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SPsimSeq: semi-parametric simulation of bulk and single-cell RNA-sequencing data.

ABSTRACT: SUMMARY:SPsimSeq is a semi-parametric simulation method to generate bulk and single-cell RNA-sequencing data. It is designed to simulate gene expression data with maximal retention of the characteristics of real data. It is reasonably flexible to accommodate a wide range of experimental scenarios, including different sample sizes, biological signals (differential expression) and confounding batch effects. AVAILABILITY AND IMPLEMENTATION:The R package and associated documentation is available from https://github.com/CenterForStatistics-UGent/SPsimSeq. SUPPLEMENTARY INFORMATION:Supplementary data are available at Bioinformatics online.

SUBMITTER: Assefa AT

PROVIDER: S-EPMC7214028 | biostudies-literature | 2020 May

REPOSITORIES: biostudies-literature

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SPsimSeq: semi-parametric simulation of bulk and single-cell RNA-sequencing data.

Assefa Alemu Takele AT Vandesompele Jo J Thas Olivier O

Bioinformatics (Oxford, England) 20200501 10

<h4>Summary</h4>SPsimSeq is a semi-parametric simulation method to generate bulk and single-cell RNA-sequencing data. It is designed to simulate gene expression data with maximal retention of the characteristics of real data. It is reasonably flexible to accommodate a wide range of experimental scenarios, including different sample sizes, biological signals (differential expression) and confounding batch effects.<h4>Availability and implementation</h4>The R package and associated documentation i ...[more]

PMID: 32065619

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