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_pkgdown.yml
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/
_pkgdown.yml
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title: Splatter
url: http://oshlacklab.com/splatter/
template:
bootstrap: 5
bootswatch: cosmo
light-switch: yes
# ganalytics: UA-52309538-4
reference:
- title: Package
desc: Package description
contents: '`splatter`'
- title: Parameters
desc: Parameters functions and classes
contents:
- '`newParams`'
- '`getParam`'
- '`getParams`'
- '`setParam`'
- '`setParams`'
- '`BASiCSParams`'
- '`KersplatParams`'
- '`Lun2Params`'
- '`LunParams`'
- '`MFAParams`'
- '`Params`'
- '`PhenoParams`'
- '`SCDDParams`'
- '`SimpleParams`'
- '`SplatParams`'
- '`SplatPopParams`'
- '`SparseDCParams`'
- '`ZINBParams`'
- title: Estimation
desc: Functions for estimating parameters
contents:
- '`BASiCSEstimate`'
- '`kersplatEstimate`'
- '`kersplatEstBCV`'
- '`kersplatEstLib`'
- '`kersplatEstMean`'
- '`lun2Estimate`'
- '`lunEstimate`'
- '`mfaEstimate`'
- '`phenoEstimate`'
- '`scDDEstimate`'
- '`simpleEstimate`'
- '`splatPopEstimate`'
- '`splatPopEstimateEffectSize`'
- '`splatPopEstimateMeanCV`'
- '`splatEstBCV`'
- '`splatEstDropout`'
- '`splatEstimate`'
- '`splatEstLib`'
- '`splatEstMean`'
- '`splatEstOutlier`'
- '`sparseDCEstimate`'
- '`zinbEstimate`'
- title: Simulation
desc: Functions for simulating datasets
- subtitle: Splat simulation
desc: Functions for the Splat simulation
contents:
- '`splatSimulate`'
- '`splatSimBatchCellMeans`'
- '`splatSimBatchEffects`'
- '`splatSimBCVMeans`'
- '`splatSimCellMeans`'
- '`splatSimDE`'
- '`splatSimDropout`'
- '`splatSimGeneMeans`'
- '`splatSimLibSizes`'
- '`splatSimTrueCounts`'
- subtitle: SplatPop simulation
desc: Functions for the SplatPop simulation
contents:
- '`splatPopSimulate`'
- '`splatPopAssignMeans`'
- '`splatPopCleanSCE`'
- '`splatPopeQTLEffects`'
- '`splatPopGroupEffects`'
- '`splatPopParseGenes`'
- '`splatPopParseVCF`'
- '`splatPopQuantNorm`'
- '`splatPopQuantNormKey`'
- '`splatPopSimEffects`'
- '`splatPopSimGeneMeans`'
- '`splatPopSimMeans`'
- '`splatPopSimulateMeans`'
- '`splatPopSimulateSample`'
- '`splatPopSimulateSC`'
- subtitle: Other simulations
desc: Functions for other simulation models
contents:
- '`BASiCSSimulate`'
- '`kersplatGenNetwork`'
- '`kersplatSample`'
- '`kersplatSelectRegs`'
- '`kersplatSetup`'
- '`kersplatSimAmbientCounts`'
- '`kersplatSimCellCounts`'
- '`kersplatSimCounts`'
- '`kersplatSimCellMeans`'
- '`kersplatSimGeneMeans`'
- '`kersplatSimLibSizes`'
- '`kersplatSimPaths`'
- '`kersplatSimulate`'
- '`lun2Simulate`'
- '`lunSimulate`'
- '`mfaSimulate`'
- '`phenoSimulate`'
- '`scDDSimulate`'
- '`simpleSimulate`'
- '`sparseDCSimulate`'
- '`zinbSimulate`'
- title: Comparison functions
desc: Functions for comparing datasets
contents:
- '`compareSCEs`'
- '`diffSCEs`'
- '`makeCompPanel`'
- '`makeDiffPanel`'
- '`makeOverallPanel`'
- '`summariseDiff`'
- title: Mock data
desc: Simple mock datasets for tests and examples
contents:
- '`mockBulkMatrix`'
- '`mockBulkeQTL`'
- '`mockEmpiricalSet`'
- '`mockGFF`'
- '`mockVCF`'
- title: Other exported functions
desc: Additional functions exported by Splatter
contents:
- '`addGeneLengths`'
- '`listSims`'
- '`minimiseSCE`'
- '`splatPopParseEmpirical`'