SPsimSeq
Semi-parametric simulation tool for bulk and single-cell RNA sequencing data
Bioconductor version: 3.23 · Package version: 1.22.0
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("SPsimSeq")Details
| Maintainer | Joris Meys <Joris.Meys@ugent.be> |
| Author | Alemu Takele Assefa [aut], Olivier Thas [ths], Joris Meys [cre], Stijn Hawinkel [aut] |
| License | GPL-2 |
| URL | https://github.com/CenterForStatistics-UGent/SPsimSeq |
| Downloads rank | 298 |
| Source branch | RELEASE_3_23 |
| biocViews | DNASeq, GeneExpression, RNASeq, Sequencing, SingleCell, Software |
Documentation
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Dependencies
Depends: R (>= 4.0)
Imports: stats, methods, SingleCellExperiment, fitdistrplus, graphics, edgeR, Hmisc, WGCNA, limma, mvtnorm, phyloseq, utils