splatter

DOI: 10.18129/B9.bioc.splatter    

Simple Simulation of Single-cell RNA Sequencing Data

Bioconductor version: Release (3.15)

Splatter is a package for the simulation of single-cell RNA sequencing count data. It provides a simple interface for creating complex simulations that are reproducible and well-documented. Parameters can be estimated from real data and functions are provided for comparing real and simulated datasets.

Author: Luke Zappia [aut, cre] , Belinda Phipson [aut] , Christina Azodi [ctb] , Alicia Oshlack [aut]

Maintainer: Luke Zappia <luke at lazappi.id.au>

Citation (from within R, enter citation("splatter")):

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("splatter")

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("splatter")

 

HTML R Script An introduction to the Splatter package
HTML R Script Splat simulation parameters
HTML R Script splatPop simulation
PDF   Reference Manual
Text   NEWS
Text   LICENSE

Details

biocViews GeneExpression, ImmunoOncology, RNASeq, Sequencing, SingleCell, Software, Transcriptomics
Version 1.20.0
In Bioconductor since BioC 3.5 (R-3.4) (5.5 years)
License GPL-3 + file LICENSE
Depends R (>= 4.0), SingleCellExperiment
Imports BiocGenerics, BiocParallel, checkmate (>= 2.0.0), edgeR, fitdistrplus, ggplot2, locfit, matrixStats, methods, scales, scater(>= 1.15.16), stats, SummarizedExperiment, utils, crayon, S4Vectors, grDevices
LinkingTo
Suggests BiocStyle, covr, cowplot, magick, knitr, limSolve, lme4, progress, pscl, testthat, preprocessCore, rmarkdown, scDD, scran, mfa, phenopath, BASiCS(>= 1.7.10), zinbwave, SparseDC, BiocManager, spelling, igraph, scuttle, BiocSingular, VariantAnnotation, Biostrings, GenomeInfoDb, GenomicRanges, IRanges
SystemRequirements
Enhances
URL https://github.com/Oshlack/splatter
BugReports https://github.com/Oshlack/splatter/issues
Depends On Me
Imports Me bcTSNE, SCRIP
Suggests Me NewWave, scone, scPCA, SummarizedBenchmark
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package splatter_1.20.0.tar.gz
Windows Binary splatter_1.20.0.zip
macOS Binary (x86_64) splatter_1.20.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/splatter
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/splatter
Package Short Url https://bioconductor.org/packages/splatter/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: