SPsimSeq
Semi-parametric simulation tool for bulk and single-cell RNA sequencing data
Bioconductor version: Release (3.20)
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 "4.4") 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 | 1.16.0 |
| In Bioconductor since | BioC 3.12 (R-4.0) (4 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 | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | SPsimSeq_1.16.0.tar.gz |
| Windows Binary (x86_64) | SPsimSeq_1.16.0.zip (64-bit only) |
| macOS Binary (x86_64) | SPsimSeq_1.16.0.tgz |
| macOS Binary (arm64) | SPsimSeq_1.15.0.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 |