SPsimSeq
This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see SPsimSeq.
Semi-parametric simulation tool for bulk and single-cell RNA sequencing data
Bioconductor version: 3.16
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")):
Installation
To install this package, start R (version "4.2") and enter:
if (!require("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")| 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 | 1.8.0 |
| 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 | |
| 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_1.8.0.tar.gz |
| Windows Binary | SPsimSeq_1.8.0.zip |
| macOS Binary (x86_64) | SPsimSeq_1.8.0.tgz |
| macOS Binary (arm64) | SPsimSeq_1.8.0.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 |
| Old Source Packages for BioC 3.16 | Source Archive |