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")):

Installation

To install this package, start R (version "4.4") 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


Reference Manual	PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DNASeq, GeneExpression, RNASeq, Sequencing, SingleCell, Software
Version	1.13.0
In Bioconductor since	BioC 3.12 (R-4.0) (3.5 years)
License	GPL-2
Depends	R (>= 4.0)
Imports	stats, methods, SingleCellExperiment, fitdistrplus, graphics, edgeR, Hmisc, WGCNA, limma, mvtnorm, phyloseq, utils
System Requirements
URL	https://github.com/CenterForStatistics-UGent/SPsimSeq

Suggests	knitr, rmarkdown, LSD, testthat, BiocStyle
Linking To
Enhances
Depends On Me
Imports Me	SurfR
Suggests Me	benchdamic
Links To Me
Build Report	Build Report

Package Archives

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

Source Package
Windows Binary
macOS Binary (x86_64)
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
Package Short Url	https://bioconductor.org/packages/SPsimSeq/
Package Downloads Report	Download Stats