splatter

DOI: 10.18129/B9.bioc.splatter    

This is the development version of splatter; for the stable release version, see splatter.

Simple Simulation of Single-cell RNA Sequencing Data

Bioconductor version: Development (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 (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 1.19.1
In Bioconductor since BioC 3.5 (R-3.4) (4.5 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, digitalDLSorteR, 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_1.19.1.tar.gz
Windows Binary
macOS 10.13 (High Sierra) splatter_1.19.1.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

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