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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 (3.19)

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

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 1.13.0
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
See More
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 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) SPsimSeq_1.13.0.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