SPsimSeq

DOI: 10.18129/B9.bioc.SPsimSeq    

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

Bioconductor version: Release (3.12)

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 "4.0") and enter:

if (!requireNamespace("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 1.0.0
In Bioconductor since BioC 3.12 (R-4.0) (< 6 months)
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
Links To Me
Build Report  

Package Archives

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

Source Package SPsimSeq_1.0.0.tar.gz
Windows Binary SPsimSeq_1.0.0.zip
macOS 10.13 (High Sierra) SPsimSeq_1.0.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/SPsimSeq
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/SPsimSeq
Package Short Url https://bioconductor.org/packages/SPsimSeq/
Package Downloads Report Download Stats

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