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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 (3.18)

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 "4.3") 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.

Documentation

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

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

Details

biocViews DNASeq, GeneExpression, RNASeq, Sequencing, SingleCell, Software
Version 1.11.0
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
Linking To
Suggests knitr, rmarkdown, LSD, testthat, BiocStyle
System Requirements
Enhances
URL https://github.com/CenterForStatistics-UGent/SPsimSeq
See More
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_1.11.0.tar.gz
Windows Binary SPsimSeq_1.11.0.zip
macOS Binary (x86_64) SPsimSeq_1.11.0.tgz
macOS Binary (arm64) SPsimSeq_1.11.0.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