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 (3.24)
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] (ORCID:
, GitHub: lazappi), Belinda Phipson [aut] (ORCID:
, GitHub: bphipson), Christina Azodi [ctb] (ORCID:
, GitHub: azodichr), Alicia Oshlack [aut]
Maintainer: Luke Zappia <luke at lazappi.id.au>
citation("splatter")):
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")
## The following initializes the development version of Bioconductor
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")| An introduction to the Splatter package | HTML | R Script |
| Splat simulation parameters | HTML | R Script |
| splatPop simulation | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | GeneExpression, ImmunoOncology, RNASeq, Sequencing, SingleCell, Software, Transcriptomics |
| Version | 1.37.1 |
| In Bioconductor since | BioC 3.5 (R-3.4) (9.5 years) |
| License | GPL-3 + file LICENSE |
| Depends | R (>= 4.0), SingleCellExperiment |
| Imports | BiocGenerics, BiocParallel, checkmate (>= 2.0.0), crayon, edgeR, fitdistrplus, grDevices, lifecycle, locfit, matrixStats, methods, rlang, S4Vectors, scrapper, scuttle, stats, SummarizedExperiment, utils, withr |
| System Requirements | |
| URL | https://bioconductor.org/packages/splatter/ https://github.com/Oshlack/splatter http://oshlacklab.com/splatter/ |
| Bug Reports | https://github.com/Oshlack/splatter/issues |
See More
| Suggests | BASiCS(>= 1.7.10), BiocManager, BiocSingular, BiocStyle, Biostrings, covr, cowplot, GenomeInfoDb, GenomicRanges, ggplot2 (>= 3.4.0), igraph, IRanges, knitr, limSolve, lme4, magick, phenopath, preprocessCore, progress, pscl, rmarkdown, scales, scater(>= 1.15.16), scDD, scran, SparseDC, spelling, testthat, VariantAnnotation, zinbwave |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | BatChef |
| Suggests Me | anglemania, ccImpute, HVP, mastR, NewWave, scone, scPCA, smartid, scellpam |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | splatter_1.37.1.tar.gz |
| Windows Binary (x86_64) | splatter_1.37.1.zip |
| macOS Binary (big-sur-x86_64) | splatter_1.37.1.tgz |
| macOS Binary (sonoma-arm64) | splatter_1.37.1.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/splatter |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/splatter |
| Bioc Package Browser | https://code.bioconductor.org/browse/splatter/ |
| Package Short Url | https://bioconductor.org/packages/splatter/ |
| Package Downloads Report | Download Stats |