API for YosefLab/MPRAnalyze
Statistical Analysis of MPRA data
| Global functions | |
|---|---|
| ChrEpi | Man page |
| MpraObject | Man page |
| MpraObject,SummarizedExperiment-method | Man page |
| MpraObject,matrix-method | Man page |
| analyzeComparative | Man page Source code |
| analyzeComparative.scale | Source code |
| analyzeQuantification | Man page Source code |
| autoChooseModel | Source code |
| ce.colAnnot | Man page |
| ce.control | Man page |
| ce.dnaCounts | Man page |
| ce.rnaCounts | Man page |
| checkForIntercept | Source code |
| compute.depth | Source code |
| controls | Man page |
| controls,MpraObject-method | Man page |
| cost.dna | Source code |
| cost.dnarna | Source code |
| cost.rna | Source code |
| cost.rna.scale | Source code |
| dnaAnnot | Man page |
| dnaAnnot,MpraObject-method | Man page |
| dnaCounts | Man page |
| dnaCounts,MpraObject-method | Man page |
| dnaDepth | Man page |
| dnaDepth,MpraObject-method | Man page |
| est.mode | Source code |
| estimateDepthFactors | Man page Source code |
| estimateFactors | Source code |
| extractModelParameters_DNA | Man page |
| extractModelParameters_RNA | Man page |
| extractProp | Source code |
| fit.dnarna.noctrlobs | Source code |
| fit.dnarna.noctrlobs.scale | Source code |
| fit.dnarna.onlyctrl.iter | Source code |
| get.ll.functions | Source code |
| getAlpha | Man page Source code |
| getDesignMat | Source code |
| getDistrParam_DNA | Man page Source code |
| getDistrParam_RNA | Man page Source code |
| getFits_DNA | Man page Source code |
| getFits_RNA | Man page Source code |
| getModelParameters_DNA | Man page Source code |
| getModelParameters_RNA | Man page Source code |
| getSingleAlpha | Source code |
| isNestedDesign | Source code |
| ll.dna.gamma.pois | Source code |
| ll.dna.ln | Source code |
| ll.rna.gamma.pois | Source code |
| ll.rna.ln.ln | Source code |
| ll.rna.ln.nb | Source code |
| ll.rna.scale.nb | Source code |
| model | Man page |
| model,MpraObject-method | Man page |
| reformatModels | Source code |
| reformatModels.scale | Source code |
| rnaAnnot | Man page |
| rnaAnnot,MpraObject-method | Man page |
| rnaCounts | Man page |
| rnaCounts,MpraObject-method | Man page |
| rnaDepth | Man page |
| rnaDepth,MpraObject-method | Man page |
| rowAnnot | Man page |
| rowAnnot,MpraObject-method | Man page |
| setDepthFactors | Man page Source code |
| setModel | Man page Source code |
| simulateMPRA | Man page Source code |
| testCoefficient | Man page Source code |
| testEmpirical | Man page Source code |
| testLrt | Man page Source code |
| testLrt.scale | Source code |
| validateMpraObject | Source code |
