SPsimSeq

This is the development version of SPsimSeq; for the stable release version, see SPsimSeq.

Semi-parametric simulation tool for bulk and single-cell RNA sequencing data

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DOI: 10.18129/B9.bioc.SPsimSeq

Bioconductor version: Development (3.23)

SPsimSeq uses a specially designed exponential family for density estimation to constructs the distribution of gene expression levels from a given real RNA sequencing data (single-cell or bulk), and subsequently simulates a new dataset from the estimated marginal distributions using Gaussian-copulas to retain the dependence between genes. It allows simulation of multiple groups and batches with any required sample size and library size.

Author: Alemu Takele Assefa [aut], Olivier Thas [ths], Joris Meys [cre], Stijn Hawinkel [aut]

Maintainer: Joris Meys <Joris.Meys at ugent.be>

Citation (from within R, enter citation("SPsimSeq")):

Installation

To install this package, start R (version "4.6") and enter:


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("SPsimSeq")

For older versions of R, please refer to the appropriate Bioconductor release.