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 (3.24)
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("SPsimSeq")):Alemu Takele Assefa, Stijn Hawinkel. SPsimSeq: Semi-parametric simulation tool for bulk and single-cell RNA sequencing data. doi:10.18129/B9.bioc.SPsimSeq, R package version 1.23.0, https://bioconductor.org/packages/SPsimSeq.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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 | ||
| NEWS | Text |
Details
| biocViews | DNASeq, GeneExpression, RNASeq, Sequencing, SingleCell, Software |
| Version | 1.23.0 |
| In Bioconductor since | BioC 3.12 (R-4.0) (6 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, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | SPsimSeq_1.23.0.tar.gz |
| Windows Binary (x86_64) | SPsimSeq_1.23.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | SPsimSeq_1.23.0.tgz |
| macOS Binary (sonoma-arm64) | SPsimSeq_1.23.0.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 |