SPsimSeq: semi-parametric simulation of bulk and single-cell RNA-sequencing data
Alemu Takele Assefa, Jo Vandesompele, Olivier Thas
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.
Topics & Concepts
Parametric statisticsComputer scienceR packageDocumentationConfoundingData miningRange (aeronautics)RNAComputational biologyGeneStatisticsBiologyMathematicsGeneticsComputational scienceEngineeringAerospace engineeringProgramming languageSingle-cell and spatial transcriptomicsCancer Genomics and DiagnosticsFerroptosis and cancer prognosis