DOI: 10.18129/B9.bioc.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

Bioconductor version: Development (3.19)

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")):


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HTML R Script Manual for the SPsimSeq package: semi-parametric simulation for bulk and single cell RNA-seq data
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biocViews DNASeq, GeneExpression, RNASeq, Sequencing, SingleCell, Software
Version 1.13.0
In Bioconductor since BioC 3.12 (R-4.0) (3 years)
License GPL-2
Depends R (>= 4.0)
Imports stats, methods, SingleCellExperiment, fitdistrplus, graphics, edgeR, Hmisc, WGCNA, limma, mvtnorm, phyloseq, utils
Suggests knitr, rmarkdown, LSD, testthat, BiocStyle
URL https://github.com/CenterForStatistics-UGent/SPsimSeq
Depends On Me
Imports Me
Suggests Me benchdamic
Links To Me
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Source Package SPsimSeq_1.13.0.tar.gz
Windows Binary SPsimSeq_1.13.0.zip
macOS Binary (x86_64) SPsimSeq_1.13.0.tgz
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/SPsimSeq
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/SPsimSeq
Bioc Package Browser https://code.bioconductor.org/browse/SPsimSeq/
Package Short Url https://bioconductor.org/packages/SPsimSeq/
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