Package: splatter 1.31.0

Luke Zappia

splatter: Simple Simulation of Single-cell RNA Sequencing Data

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.

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

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splatter.pdf |splatter.html✨
splatter/json (API)
NEWS

# Install 'splatter' in R:

install.packages('splatter', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/oshlack/splatter/issues

On BioConductor:splatter-1.31.0(bioc 3.21)splatter-1.30.0(bioc 3.20)

singlecell rnaseq transcriptomics geneexpression sequencing software immunooncology bioconductor bioinformatics scrna-seq simulation

9.75 score 217 stars 1 packages 414 scripts 801 downloads 6 mentions 63 exports 54 dependencies

Last updated 21 days agofrom:77f3611a1c. Checks:ERROR: 2 WARNING: 5. Indexed: yes.

Target	Result	Date
Doc / Vignettes	FAIL	Nov 18 2024
R-4.5-win	WARNING	Nov 18 2024
R-4.5-linux	ERROR	Nov 18 2024
R-4.4-win	WARNING	Nov 18 2024
R-4.4-mac	WARNING	Nov 18 2024
R-4.3-win	WARNING	Nov 18 2024
R-4.3-mac	WARNING	Nov 18 2024

Exports:addGeneLengths BASiCSEstimate BASiCSSimulate compareSCEs diffSCEs getParam getParams kersplatEstimate kersplatSample kersplatSetup kersplatSimulate listSims lun2Estimate lun2Simulate lunEstimate lunSimulate makeCompPanel makeDiffPanel makeOverallPanel mfaEstimate mfaSimulate minimiseSCE mockBulkeQTL mockBulkMatrix mockEmpiricalSet mockGFF mockVCF newBASiCSParams newKersplatParams newLun2Params newLunParams newMFAParams newPhenoParams newSCDDParams newSimpleParams newSparseDCParams newSplatParams newSplatPopParams newZINBParams phenoEstimate phenoSimulate scDDEstimate scDDSimulate setParam setParams simpleEstimate simpleSimulate sparseDCEstimate sparseDCSimulate splatEstimate splatPopEstimate splatPopParseEmpirical splatPopQuantNorm splatPopSimulate splatPopSimulateMeans splatPopSimulateSC splatSimulate splatSimulateGroups splatSimulatePaths splatSimulateSingle summariseDiff zinbEstimate zinbSimulate

Dependencies:abind askpass assorthead backports beachmat BH Biobase BiocGenerics BiocParallel checkmate codetools cpp11 crayon curl DelayedArray edgeR fitdistrplus formatR futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicRanges httr IRanges jsonlite lambda.r lattice limma locfit MASS Matrix MatrixGenerics matrixStats mime openssl R6 Rcpp rlang S4Arrays S4Vectors scuttle SingleCellExperiment snow SparseArray statmod SummarizedExperiment survival sys UCSC.utils withr XVector zlibbioc

Vignettes and/or manual for this package failed to build, some documents may be unavailable. Please inspect thebuild logs for more information.

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Add gene lengths	addGeneLengths
Estimate BASiCS simulation parameters	BASiCSEstimate BASiCSEstimate.matrix BASiCSEstimate.SingleCellExperiment
The BASiCSParams class	BASiCSParams BASiCSParams-class
BASiCS simulation	BASiCSSimulate
Compare SingleCellExperiment objects	compareSCEs
Diff SingleCellExperiment objects	diffSCEs
Get a parameter	getParam getParam,Params-method
Get parameters	getParams
Estimate Kersplat simulation parameters	kersplatEstimate kersplatEstimate.matrix kersplatEstimate.SingleCellExperiment
The KersplatParams class	KersplatParams KersplatParams-class
Kersplat sample	kersplatSample
Kersplat setup	kersplatSetup
Kersplat simulation	kersplatSimulate
List simulations	listSims
Estimate Lun2 simulation parameters	lun2Estimate lun2Estimate.matrix lun2Estimate.SingleCellExperiment
The Lun2Params class	Lun2Params Lun2Params-class
Lun2 simulation	lun2Simulate
Estimate Lun simulation parameters	lunEstimate lunEstimate.matrix lunEstimate.SingleCellExperiment
The LunParams class	LunParams LunParams-class
Lun simulation	lunSimulate
Make comparison panel	makeCompPanel
Make difference panel	makeDiffPanel
Make overall panel	makeOverallPanel
Estimate mfa simulation parameters	mfaEstimate mfaEstimate.matrix mfaEstimate.SingleCellExperiment
The MFAParams class	MFAParams MFAParams-class
MFA simulation	mfaSimulate
Minimise SCE	minimiseSCE
Generate mock eQTL mapping results	mockBulkeQTL
Generate mock bulk population scale expression data	mockBulkMatrix
Generate set of "empirical" mock data	mockEmpiricalSet
Generate mock gff	mockGFF
Generate mock vcf	mockVCF
New Params	newBASiCSParams newKersplatParams newLun2Params newLunParams newMFAParams newParams newPhenoParams newSCDDParams newSimpleParams newSparseDCParams newSplatParams newSplatPopParams newZINBParams
The Params virtual class	Params Params-class
Estimate PhenoPath simulation parameters	phenoEstimate phenoEstimate.matrix phenoEstimate.SingleCellExperiment
The PhenoParams class	PhenoParams PhenoParams-class
PhenoPath simulation	phenoSimulate
Estimate scDD simulation parameters	scDDEstimate scDDEstimate.default scDDEstimate.matrix scDDEstimate.SingleCellExperiment
The SCDDParams class	SCDDParams SCDDParams-class
scDD simulation	scDDSimulate
Set a parameter	setParam setParam,BASiCSParams-method setParam,KersplatParams-method setParam,Lun2Params-method setParam,LunParams-method setParam,Params-method setParam,PhenoParams-method setParam,SCDDParams-method setParam,SplatParams-method setParam,SplatPopParams-method setParam,ZINBParams-method
Set parameters	setParams setParams,KersplatParams-method setParams,Params-method setParams,SplatParams-method
Estimate simple simulation parameters	simpleEstimate simpleEstimate.matrix simpleEstimate.SingleCellExperiment
The SimpleParams class	SimpleParams SimpleParams-class
Simple simulation	simpleSimulate
Estimate SparseDC simulation parameters	sparseDCEstimate sparseDCEstimate.matrix sparseDCEstimate.SingleCellExperiment
The SparseDCParams class	SparseDCParams SparseDCParams-class
SparseDC simulation	sparseDCSimulate
Estimate Splat simulation parameters	splatEstimate splatEstimate.matrix splatEstimate.SingleCellExperiment
The SplatParams class	SplatParams SplatParams-class
Estimate population/eQTL simulation parameters	splatPopEstimate
The SplatPopParams class	SplatPopParams SplatPopParams-class
splatPopParseEmpirical	splatPopParseEmpirical
Quantile normalize by sample to fit sc expression distribution.	splatPopQuantNorm
splatPop simulation	splatPopSimulate
splatPopSimulateMeans	splatPopSimulateMeans
splatPopSimulateSC	splatPopSimulateSC
Splat simulation	splatSimulate splatSimulateGroups splatSimulatePaths splatSimulateSingle
Summarise diffSCEs	summariseDiff
Estimate ZINB-WaVE simulation parameters	zinbEstimate zinbEstimate.matrix zinbEstimate.SingleCellExperiment
The ZINBParams class	ZINBParams ZINBParams-class
ZINB-WaVE simulation	zinbSimulate