API for heiniglab/scPower
Experimental design framework for scRNAseq population studies (eQTL and DE)
| Global functions | |
|---|---|
| AIC | Source code |
| BIC | Source code |
| CDF | Source code |
| CDF.Gamma | Source code |
| CDF.LeftCensoredGamma | Source code |
| CDF.Negbinom | Source code |
| EMPosterior | Source code |
| TruncatedDistribution | Source code |
| annot.df | Man page |
| annot_smartseq | Man page |
| budget.optimization | Man page |
| budgetCalculation | Man page Source code |
| budgetCalculation.libPrepCell | Man page Source code |
| budgetCalculation.restrictedDoublets | Man page Source code |
| calculate.gene.counts | Man page Source code |
| calculate.probabilities | Man page Source code |
| cellsBudgetCalculation | Man page Source code |
| cellsBudgetCalculation.libPrepCell | Man page Source code |
| cellsBudgetCalculation.restrictedDoublets | Man page Source code |
| convert.gamma.parameters | Man page Source code |
| count.matrix.example | Man page |
| counts_smartseq | Man page |
| create.pseudobulk | Man page Source code |
| de.ref.study | Man page |
| disp.fun.param | Man page |
| disp.fun.param.drop | Man page |
| disp.fun.param.smart | Man page |
| dispersion.function.estimation | Man page Source code |
| drawFrom | Source code |
| drawFrom.Gamma | Source code |
| drawFrom.LeftCensoredGamma | Source code |
| drawFrom.Negbinom | Source code |
| drawFrom.TruncatedDistribution | Source code |
| drawFrom.Zero | Source code |
| drawFrom.Zinba | Source code |
| effectSize.DE.simulation | Man page Source code |
| effectSize.eQTL.simulation | Man page Source code |
| em | Source code |
| eqtl.ref.study | Man page |
| estimate.exp.prob.count.param | Man page Source code |
| estimate.exp.prob.param | Man page Source code |
| estimate.exp.prob.values | Man page Source code |
| estimate.mean.dsp.values | Man page Source code |
| estimate.size.simulation | Man page Source code |
| fdr.optimization | Man page Source code |
| fit | Source code |
| fit.CZinba | Source code |
| fit.Gamma | Source code |
| fit.LeftCensoredGamma | Source code |
| fit.LogNormal | Source code |
| fit.Negbinom | Source code |
| fit.TruncatedDistribution | Source code |
| fit.Zero | Source code |
| fit.Zinba | Source code |
| fit.ZinbaCopula | Source code |
| gamma.mixed.fits | Man page |
| gamma.mixed.fits.drop | Man page |
| gamma.mixed.fits.smart | Man page |
| gene.rank.calculation | Man page Source code |
| gene.rank.calculation.vector | Man page Source code |
| gene_length | Man page |
| logLikelihood | Source code |
| logLikelihood.CZinba | Source code |
| logLikelihood.EMResult | Source code |
| logLikelihood.Gamma | Source code |
| logLikelihood.LeftCensoredGamma | Source code |
| logLikelihood.LogNormal | Source code |
| logLikelihood.Negbinom | Source code |
| logLikelihood.TruncatedDistribution | Source code |
| logLikelihood.Zero | Source code |
| logLikelihood.Zinba | Source code |
| logLikelihood.ZinbaCopula | Source code |
| logsum | Source code |
| meanUMI.calculation | Man page Source code |
| mixed.gamma.estimation | Man page Source code |
| nbinom.estimation | Man page Source code |
| nparam | Source code |
| nparam.EMResult | Source code |
| nparam.Zero | Source code |
| number.cells.detect.celltype | Man page Source code |
| observed.gene.counts | Man page |
| optimize.constant.budget | Man page Source code |
| optimize.constant.budget.libPrepCell | Man page Source code |
| optimize.constant.budget.restrictedDoublets | Man page Source code |
| optimize.constant.budget.smartseq | Man page Source code |
| optimizeSizeFactor | Man page Source code |
| parametricDispersionFit_DEseq | Man page Source code |
| plotDensity | Source code |
| plotDensity.Distribution | Source code |
| plotDensity.EMResult | Source code |
| power.de | Man page Source code |
| power.detect.celltype | Man page Source code |
| power.eqtl | Man page Source code |
| power.eqtl.ftest | Man page Source code |
| power.eqtl.simulated | Man page Source code |
| power.eqtl.simulated.help | Man page Source code |
| power.general.restrictedDoublets | Man page Source code |
| power.general.withDoublets | Man page Source code |
| power.sameReadDepth.restrictedDoublets | Man page Source code |
| power.sameReadDepth.withDoublets | Man page Source code |
| power.smartseq | Man page Source code |
| print_optimalDesign_10X | Man page Source code |
| read.umi.fit | Man page |
| readDepthBudgetCalculation | Man page Source code |
| readDepthBudgetCalculation.libPrepCell | Man page Source code |
| readDepthBudgetCalculation.restrictedDoublets | Man page Source code |
| runShiny | Man page Source code |
| sample.disp.values | Man page Source code |
| sample.mean.values.quantiles | Man page Source code |
| sample.mean.values.random | Man page Source code |
| sampleSizeBudgetCalculation | Man page Source code |
| sampleSizeBudgetCalculation.libPrepCell | Man page Source code |
| sampleSizeBudgetCalculation.restrictedDoublets | Man page Source code |
| select.cutoffs | Man page Source code |
| sim.eqtl.pvals | Man page |
| simulated.DE.values | Man page |
| simulated.eQTL.values | Man page |
| size.estimates | Man page |
| sizeFactorsPosCounts | Man page Source code |
| sizeFactorsStandard | Man page Source code |
| truncate | Source code |
| umi.gamma.relation | Man page Source code |
| umi.read.relation | Man page Source code |
| uniform.ranks.interval | Man page Source code |
| visualize.gamma.fits | Man page Source code |
| visualize.power.grid | Man page Source code |
