Man pages for Oshlack/splatter
Simple Simulation of Single-cell RNA Sequencing Data
| addGeneLengths | Add gene lengths |
| BASiCSEstimate | Estimate BASiCS simulation parameters |
| BASiCSParams | The BASiCSParams class |
| BASiCSSimulate | BASiCS simulation |
| compareSCEs | Compare SingleCellExperiment objects |
| diffSCEs | Diff SingleCellExperiment objects |
| expandParams | Expand parameters |
| getLNormFactors | Get log-normal factors |
| getParam | Get a parameter |
| getParams | Get parameters |
| kersplatEstBCV | Estimate Kersplat BCV parameters |
| kersplatEstimate | Estimate Kersplat simulation parameters |
| kersplatEstLib | Estimate Kersplat library size parameters |
| kersplatEstMean | Estimate Kersplat means |
| kersplatGenNetwork | Generate Kersplat gene network |
| KersplatParams | 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 |
| lun2Estimate | Estimate Lun2 simulation parameters |
| Lun2Params | The Lun2Params class |
| lun2Simulate | Lun2 simulation |
| lunEstimate | Estimate Lun simulation parameters |
| LunParams | The LunParams class |
| lunSimulate | Lun simulation |
| makeCompPanel | Make comparison panel |
| makeDiffPanel | Make difference panel |
| makeOverallPanel | Make overall panel |
| mfaEstimate | Estimate mfa simulation parameters |
| MFAParams | 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 |
| newParams | New Params |
| Params | The Params virtual class |
| phenoEstimate | Estimate PhenoPath simulation parameters |
| PhenoParams | The PhenoParams class |
| phenoSimulate | PhenoPath simulation |
| scDDEstimate | Estimate scDD simulation parameters |
| SCDDParams | The SCDDParams class |
| scDDSimulate | scDD simulation |
| setParam | Set a parameter |
| setParams | Set parameters |
| setParamsUnchecked | Set parameters UNCHECKED |
| setParamUnchecked | Set a parameter UNCHECKED |
| simpleEstimate | Estimate simple simulation parameters |
| SimpleParams | The SimpleParams class |
| simpleSimulate | Simple simulation |
| sparseDCEstimate | Estimate SparseDC simulation parameters |
| SparseDCParams | The SparseDCParams class |
| sparseDCSimulate | SparseDC simulation |
| splatEstBCV | Estimate Splat Biological Coefficient of Variation parameters |
| splatEstDropout | Estimate Splat dropout parameters |
| splatEstimate | 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 |
| splatPopAssignMeans | Sample expression mean and variance for each gene |
| splatPopCleanSCE | Clean up the population-scale SCE to remove redundant... |
| 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 |
| splatPopParseEmpirical | splatPopParseEmpirical |
| splatPopParseGenes | Generate population key matrix from random or gff provided... |
| splatPopParseVCF | Format and subset genotype data from a VCF file. |
| splatPopQuantNorm | Quantile normalize by sample to fit sc expression... |
| 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 |
| splatSimLibSizes | Simulate library sizes |
| splatSimTrueCounts | Simulate true counts |
| splatSimulate | Splat simulation |
| splatter-package | splatter: Simple Simulation of Single-cell RNA Sequencing... |
| summariseDiff | Summarise diffSCEs |
| zinbEstimate | Estimate ZINB-WaVE simulation parameters |
| ZINBParams | The ZINBParams class |
| zinbSimulate | ZINB-WaVE simulation |
