SPsimSeq
This is the released version of SPsimSeq; for the devel version, see SPsimSeq.
Semi-parametric simulation tool for bulk and single-cell RNA sequencing data
Bioconductor version: Release (3.23)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | 1.22.0 |
| 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 |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | SPsimSeq_1.22.0.tar.gz |
| Windows Binary (x86_64) | SPsimSeq_1.22.0.zip |
| macOS Binary (big-sur-x86_64) | SPsimSeq_1.22.0.tgz |
| macOS Binary (sonoma-arm64) | SPsimSeq_1.22.0.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 |