Simple Simulation of Single-cell RNA Sequencing Data
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Documentation for package ‘splatter’ version 1.28.0
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-- A --
| addGeneLengths | Add gene lengths |
-- B --
| BASiCSEstimate | Estimate BASiCS simulation parameters |
| BASiCSEstimate.matrix | Estimate BASiCS simulation parameters |
| BASiCSEstimate.SingleCellExperiment | Estimate BASiCS simulation parameters |
| BASiCSParams | The BASiCSParams class |
| BASiCSParams-class | The BASiCSParams class |
| BASiCSSimulate | BASiCS simulation |
-- C --
| compareSCEs | Compare SingleCellExperiment objects |
-- D --
| diffSCEs | Diff SingleCellExperiment objects |
-- G --
| getParam | Get a parameter |
| getParam-method | Get a parameter |
| getParams | Get parameters |
-- K --
| kersplatEstimate | Estimate Kersplat simulation parameters |
| kersplatEstimate.matrix | Estimate Kersplat simulation parameters |
| kersplatEstimate.SingleCellExperiment | Estimate Kersplat simulation parameters |
| KersplatParams | The KersplatParams class |
| KersplatParams-class | The KersplatParams class |
| kersplatSample | Kersplat sample |
| kersplatSetup | Kersplat setup |
| kersplatSimulate | Kersplat simulation |
-- L --
| listSims | List simulations |
| lun2Estimate | Estimate Lun2 simulation parameters |
| lun2Estimate.matrix | Estimate Lun2 simulation parameters |
| lun2Estimate.SingleCellExperiment | Estimate Lun2 simulation parameters |
| Lun2Params | The Lun2Params class |
| Lun2Params-class | The Lun2Params class |
| lun2Simulate | Lun2 simulation |
| lunEstimate | Estimate Lun simulation parameters |
| lunEstimate.matrix | Estimate Lun simulation parameters |
| lunEstimate.SingleCellExperiment | Estimate Lun simulation parameters |
| LunParams | The LunParams class |
| LunParams-class | The LunParams class |
| lunSimulate | Lun simulation |
-- M --
| makeCompPanel | Make comparison panel |
| makeDiffPanel | Make difference panel |
| makeOverallPanel | Make overall panel |
| mfaEstimate | Estimate mfa simulation parameters |
| mfaEstimate.matrix | Estimate mfa simulation parameters |
| mfaEstimate.SingleCellExperiment | Estimate mfa simulation parameters |
| MFAParams | The MFAParams class |
| MFAParams-class | The MFAParams class |
| mfaSimulate | MFA simulation |
| minimiseSCE | Minimise SCE |
| mockBulkeQTL | Generate mock eQTL mapping results |
| mockBulkMatrix | Generate mock bulk population scale expression data |
| mockEmpiricalSet | Generate set of "empirical" mock data |
| mockGFF | Generate mock gff |
| mockVCF | Generate mock vcf |
-- N --
| newBASiCSParams | New Params |
| newKersplatParams | New Params |
| newLun2Params | New Params |
| newLunParams | New Params |
| newMFAParams | New Params |
| newParams | New Params |
| newPhenoParams | New Params |
| newSCDDParams | New Params |
| newSimpleParams | New Params |
| newSparseDCParams | New Params |
| newSplatParams | New Params |
| newSplatPopParams | New Params |
| newZINBParams | New Params |
-- P --
| Params | The Params virtual class |
| Params-class | The Params virtual class |
| phenoEstimate | Estimate PhenoPath simulation parameters |
| phenoEstimate.matrix | Estimate PhenoPath simulation parameters |
| phenoEstimate.SingleCellExperiment | Estimate PhenoPath simulation parameters |
| PhenoParams | The PhenoParams class |
| PhenoParams-class | The PhenoParams class |
| phenoSimulate | PhenoPath simulation |
-- S --
| scDDEstimate | Estimate scDD simulation parameters |
| scDDEstimate.default | Estimate scDD simulation parameters |
| scDDEstimate.matrix | Estimate scDD simulation parameters |
| scDDEstimate.SingleCellExperiment | Estimate scDD simulation parameters |
| SCDDParams | The SCDDParams class |
| SCDDParams-class | The SCDDParams class |
| scDDSimulate | scDD simulation |
| setParam | Set a parameter |
| setParam-method | Set a parameter |
| setParams | Set parameters |
| setParams-method | Set parameters |
| simpleEstimate | Estimate simple simulation parameters |
| simpleEstimate.matrix | Estimate simple simulation parameters |
| simpleEstimate.SingleCellExperiment | Estimate simple simulation parameters |
| SimpleParams | The SimpleParams class |
| SimpleParams-class | The SimpleParams class |
| simpleSimulate | Simple simulation |
| sparseDCEstimate | Estimate SparseDC simulation parameters |
| sparseDCEstimate.matrix | Estimate SparseDC simulation parameters |
| sparseDCEstimate.SingleCellExperiment | Estimate SparseDC simulation parameters |
| SparseDCParams | The SparseDCParams class |
| SparseDCParams-class | The SparseDCParams class |
| sparseDCSimulate | SparseDC simulation |
| splatEstimate | Estimate Splat simulation parameters |
| splatEstimate.matrix | Estimate Splat simulation parameters |
| splatEstimate.SingleCellExperiment | Estimate Splat simulation parameters |
| SplatParams | The SplatParams class |
| SplatParams-class | The SplatParams class |
| splatPopEstimate | Estimate population/eQTL simulation parameters |
| SplatPopParams | The SplatPopParams class |
| SplatPopParams-class | The SplatPopParams class |
| splatPopParseEmpirical | splatPopParseEmpirical |
| splatPopQuantNorm | Quantile normalize by sample to fit sc expression distribution. |
| splatPopSimulate | splatPop simulation |
| splatPopSimulateMeans | splatPopSimulateMeans |
| splatPopSimulateSC | splatPopSimulateSC |
| splatSimulate | Splat simulation |
| splatSimulateGroups | Splat simulation |
| splatSimulatePaths | Splat simulation |
| splatSimulateSingle | Splat simulation |
| summariseDiff | Summarise diffSCEs |
-- Z --
| zinbEstimate | Estimate ZINB-WaVE simulation parameters |
| zinbEstimate.matrix | Estimate ZINB-WaVE simulation parameters |
| zinbEstimate.SingleCellExperiment | Estimate ZINB-WaVE simulation parameters |
| ZINBParams | The ZINBParams class |
| ZINBParams-class | The ZINBParams class |
| zinbSimulate | ZINB-WaVE simulation |