SPsimSeq

DOI: 10.18129/B9.bioc.SPsimSeq  

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

Bioconductor version: Release (3.16)

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>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("SPsimSeq")

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

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("SPsimSeq")

 

HTML	R Script	Manual for the SPsimSeq package: semi-parametric simulation for bulk and single cell RNA-seq data
PDF		Reference Manual
Text		NEWS

Details

biocViews	DNASeq, GeneExpression, RNASeq, Sequencing, SingleCell, Software
Version	1.8.0
In Bioconductor since	BioC 3.12 (R-4.0) (2.5 years)
License	GPL-2
Depends	R (>= 4.0)
Imports	stats, methods, SingleCellExperiment, fitdistrplus, graphics, edgeR, Hmisc, WGCNA, limma, mvtnorm, phyloseq, utils
LinkingTo
Suggests	knitr, rmarkdown, LSD, testthat, BiocStyle
SystemRequirements
Enhances
URL	https://github.com/CenterForStatistics-UGent/SPsimSeq
Depends On Me
Imports Me
Suggests Me	benchdamic
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	SPsimSeq_1.8.0.tar.gz
Windows Binary	SPsimSeq_1.8.0.zip
macOS Binary (x86_64)	SPsimSeq_1.8.0.tgz
macOS Binary (arm64)	SPsimSeq_1.8.0.tgz
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/
Package Downloads Report	Download Stats