API for IMB-Computational-Genomics-Lab/ascend
ascend - Analysis of Single Cell Expression, Normalisation, and Differential expression
| Global functions | |
|---|---|
| .EMSet | Man page |
| EMSet | Man page Source code |
| EMSet-class | Man page |
| [,EMSet,ANY,ANY,ANY-method | Man page |
| [<-,EMSet,ANY,ANY,EMSet-method | Man page |
| addGeneLabel | Man page |
| addGeneLabel,EMSet-method | Man page |
| analyzed_set | Man page |
| ascend | Man page |
| ascend-package | Man page |
| bimodLikData | Source code |
| bimodLikData_FixNoVar | Source code |
| buildKeyStat | Source code |
| calcControlQC | Source code |
| calcGeoMeansDense | Man page Source code |
| calcGeoMeansSparse | Man page Source code |
| calcNormFactorDense | Man page Source code |
| calcNormFactorSparse | Man page Source code |
| calcRandIndexMatrix | Source code |
| calcStability | Source code |
| calcVariance | Source code |
| calculateCV | Man page |
| calculateCV,EMSet-method | Man page |
| calculateControlMetrics | Source code |
| calculateQC | Man page |
| calculateQC,EMSet-method | Man page |
| chooseNew | Source code |
| clusterAnalysis | Man page |
| clusterAnalysis,EMSet-method | Man page |
| clusterAnalysis<- | Man page |
| clusterAnalysis<-,EMSet-method | Man page |
| colInfo | Man page |
| colInfo,EMSet-method | Man page |
| colInfo<- | Man page |
| colInfo<-,EMSet-method | Man page |
| controls | Man page |
| controls,EMSet-method | Man page |
| controls<- | Man page |
| controls<-,EMSet-method | Man page |
| convert | Man page Source code |
| convertEMSetToSeurat | Source code |
| convertGeneID | Man page |
| convertGeneID,EMSet-method | Man page |
| convertSCEtoEMSet | Source code |
| convertSeuratToEMSet | Source code |
| convertSparse | Man page Source code |
| convertToSCE | Source code |
| convertToScone | Source code |
| differentialLRT | Source code |
| excludeControl | Man page |
| excludeControl,EMSet-method | Man page |
| fileCheck | Source code |
| filterByControl | Man page Source code |
| filterByOutliers | Man page Source code |
| filterLowAbundanceGenes | Man page Source code |
| findOptimalResult | Source code |
| func_DESeq | Man page Source code |
| getConsecSeq | Source code |
| joinPaths | Source code |
| loadCellRanger | Man page Source code |
| loadCounts | Source code |
| mergeDF | Source code |
| minMax | Source code |
| normaliseBatches | Man page Source code |
| normaliseByRLE | Man page Source code |
| plotAverageGeneCount | Man page Source code |
| plotBatchNormQC | Man page Source code |
| plotControlHist | Man page Source code |
| plotControlPctPerSample | Man page Source code |
| plotDendrogram | Man page Source code |
| plotFeatureHist | Man page Source code |
| plotGeneNumber | Man page Source code |
| plotGeneralQC | Man page Source code |
| plotLibsizeBoxplot | Man page Source code |
| plotLibsizeHist | Man page Source code |
| plotLibsizePerSample | Man page Source code |
| plotMDS | Man page Source code |
| plotNormQC | Man page Source code |
| plotPCA | Man page Source code |
| plotPCAVariance | Man page Source code |
| plotSmoothScatter | Man page Source code |
| plotStability | Man page Source code |
| plotStabilityDendro | Man page Source code |
| plotTSNE | Man page Source code |
| plotTopGenesBoxplot | Man page Source code |
| plotTopGenesPerSample | Man page Source code |
| plotUMAP | Man page Source code |
| plotVariableGenes | Man page Source code |
| plotVolcano | Man page Source code |
| progressLog | Man page |
| progressLog,EMSet-method | Man page |
| progressLog<- | Man page |
| progressLog<-,EMSet-method | Man page |
| raw | Man page |
| raw_set | Man page |
| regcounts | Man page |
| regcounts,EMSet-method | Man page |
| regcounts<- | Man page |
| regcounts<-,EMSet-method | Man page |
| regressConfoundingFactors | Man page Source code |
| regressGene | Source code |
| retrieveCluster | Source code |
| rowInfo | Man page |
| rowInfo,EMSet-method | Man page |
| rowInfo<- | Man page |
| rowInfo<-,EMSet-method | Man page |
| runCORE | Man page |
| runCORE,EMSet-method | Man page |
| runDESeq | Man page Source code |
| runDESeq2 | Man page Source code |
| runDiffExpression | Man page Source code |
| runGeneLRT | Source code |
| runPCA | Man page |
| runPCA,EMSet-method | Man page |
| runTSNE | Man page |
| runTSNE,EMSet-method | Man page |
| runUMAP | Man page |
| runUMAP,EMSet-method | Man page |
| scranCellCycle | Man page Source code |
| scranNormalise | Man page Source code |
| show,EMSet-method | Man page |
| subsetCondition | Man page |
| subsetCondition,EMSet-method | Man page |
| unLog2Matrix | Source code |
| updateObject,EMSet-method | Man page |
| useVariableGenes | Man page |
| useVariableGenes,EMSet-method | Man page |
| validateEMSet | Man page Source code |
| worker_LRT | Source code |
