A B C D E G K L M N P R S T W Z
| addFeatureStats | Add feature statistics |
| addGeneLengths | Add gene lengths |
| 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 |
| bridge | Brownian bridge |
| bringItemsForward | Bring items forward |
| checkDependencies | Check dependencies |
| co.var | Calculate coefficient of variation |
| compareSCEs | Compare SingleCellExperiment objects |
| diffSCEs | Diff SingleCellExperiment objects |
| expandParams | Expand parameters |
| expandParams-method | Expand parameters |
| getBetaStepProbs | Get Beta step probabilities |
| getCounts | Get counts |
| getLNormFactors | Get log-normal factors |
| getParam | Get a parameter |
| getParam-method | Get a parameter |
| getParams | Get parameters |
| getPathOrder | Get path order |
| kersplatEstBCV | Estimate Kersplat BCV parameters |
| kersplatEstimate | Estimate Kersplat simulation parameters |
| kersplatEstimate.matrix | Estimate Kersplat simulation parameters |
| kersplatEstimate.SingleCellExperiment | Estimate Kersplat simulation parameters |
| kersplatEstLib | Estimate Kersplat library size parameters |
| kersplatEstMean | Estimate Kersplat means |
| kersplatGenNetwork | Generate Kersplat gene network |
| KersplatParams | The KersplatParams class |
| KersplatParams-class | The KersplatParams class |
| kersplatSample | Kersplat sample |
| kersplatSelectRegs | Select Kersplat regulators |
| kersplatSetup | Kersplat setup |
| kersplatSimAmbientCounts | Simulate Kersplat ambient counts |
| kersplatSimCellCounts | Simulate Kersplat cell counts |
| kersplatSimCellMeans | Simulate Kersplat cell means |
| kersplatSimCounts | Simulate Kersplat final counts |
| kersplatSimGeneMeans | Simulate Kersplat gene means |
| kersplatSimLibSizes | Simulate Kersplat library sizes |
| kersplatSimPaths | Simulate Kersplat paths |
| kersplatSimulate | Kersplat simulation |
| listSims | List simulations |
| logistic | Logistic function |
| 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 |
| 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 |
| 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 |
| Params | The Params virtual class |
| Params-class | The Params virtual class |
| paramsExpander | Expand parameters |
| 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 |
| rbindMatched | Bind rows (matched) |
| sampleDensity | Sample density |
| 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 |
| selectFit | Select fit |
| setParam | Set a parameter |
| setParam-method | Set a parameter |
| setParams | Set parameters |
| setParams-method | Set parameters |
| setParamsUnchecked | Set parameters UNCHECKED |
| setParamUnchecked | Set a parameter UNCHECKED |
| setParamUnchecked-method | Set a parameter UNCHECKED |
| showDFs | Show data.frame |
| showPP | Show pretty print |
| showValues | Show values |
| 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 |
| sparsifyMatrices | Sparsify matrices |
| splatEstBCV | Estimate Splat Biological Coefficient of Variation parameters |
| splatEstDropout | Estimate Splat dropout parameters |
| splatEstimate | Estimate Splat simulation parameters |
| splatEstimate.matrix | Estimate Splat simulation parameters |
| splatEstimate.SingleCellExperiment | Estimate Splat simulation parameters |
| splatEstLib | Estimate Splat library size parameters |
| splatEstMean | Estimate Splat mean parameters |
| splatEstOutlier | Estimate Splat expression outlier parameters |
| SplatParams | The SplatParams class |
| SplatParams-class | The SplatParams class |
| splatPopAssignMeans | Sample expression mean and variance for each gene |
| splatPopCleanSCE | Clean up the population-scale SCE to remove redundant information |
| splatPopConditionalEffects | Add conditional DE effects to means matrix |
| splatPopConditionEffects | Assign Condition-specific eQTL and DEGs. |
| splatPopDesignBatches | Set up pooled experimental design |
| splatPopDesignConditions | Set up designed experiments conditions |
| splatPopeQTLEffects | Assign eGenes-eSNPs pairs and effect sizes. |
| splatPopEstimate | Estimate population/eQTL simulation parameters |
| splatPopEstimateEffectSize | Estimate eQTL Effect Size parameters |
| splatPopEstimateMeanCV | Estimate gene mean and gene mean variance parameters |
| splatPopGroupEffects | Assign group-specific eQTL and DEGs. |
| SplatPopParams | The SplatPopParams class |
| SplatPopParams-class | The SplatPopParams class |
| splatPopParseEmpirical | splatPopParseEmpirical |
| splatPopParseGenes | Generate population key matrix from random or gff provided gene information |
| splatPopParseVCF | Format and subset genotype data from a VCF file. |
| splatPopQuantNorm | Quantile normalize by sample to fit sc expression distribution. |
| splatPopQuantNormKey | Add quantile normalized gene mean and cv info the eQTL key. |
| splatPopSimBatchEffects | Simulate batch effects |
| splatPopSimConditionalEffects | Add conditional DE effects to means matrix |
| splatPopSimEffects | Add eQTL effects to means matrix |
| splatPopSimGeneMeans | Simulate gene means for splatPop |
| splatPopSimMeans | Simulate mean gene expression matrix without eQTL effects |
| splatPopSimulate | splatPop simulation |
| splatPopSimulateMeans | splatPopSimulateMeans |
| splatPopSimulateSample | splatPopSimulateSample simulation |
| splatPopSimulateSC | splatPopSimulateSC |
| splatSimBatchCellMeans | Simulate batch means |
| splatSimBatchEffects | Simulate batch effects |
| splatSimBCVMeans | Simulate BCV means |
| splatSimCellMeans | Simulate cell means |
| splatSimDE | Simulate group differential expression |
| splatSimDropout | Simulate dropout |
| splatSimGeneMeans | Simulate gene means |
| splatSimGroupCellMeans | Simulate cell means |
| splatSimGroupDE | Simulate group differential expression |
| splatSimLibSizes | Simulate library sizes |
| splatSimPathCellMeans | Simulate cell means |
| splatSimPathDE | Simulate group differential expression |
| splatSimSingleCellMeans | Simulate cell means |
| splatSimTrueCounts | Simulate true counts |
| splatSimulate | Splat simulation |
| splatSimulateGroups | Splat simulation |
| splatSimulatePaths | Splat simulation |
| splatSimulateSingle | Splat simulation |
| splatter | splatter. |
| summariseDiff | Summarise diffSCEs |
| summariseKS | Summarise KS |
| summariseStats | Summarise statistics |
| tidyStatSumm | Tidy summarised statistics |
| winsorize | Winsorize vector |
| 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 |