Man pages for IMB-Computational-Genomics-Lab/ascend
ascend - Analysis of Single Cell Expression, Normalisation, and Differential expression
| addGeneLabel | addGeneLabel |
| analyzed_set | Retinal Ganglion Cells (100 THY-1 positive, 100 THY-1... |
| ascend | ascend A package for the quality control and analysis of... |
| calcGeoMeansDense | Calculate geometric means for dense matrices |
| calcGeoMeansSparse | Calculate geometric means of sparse matrices |
| calcNormFactorDense | Calculate size factors for dense matrices |
| calcNormFactorSparse | Calculate size factors from sparse matrices |
| calculateCV | calculateCV |
| calculateQC | calculateQC |
| clusterAnalysis | clusterAnalysis |
| colInfo | colInfo |
| controls | controls |
| convert | convert |
| convertGeneID | convertGeneID |
| convertSparse | Convert R sparse matrix to RcppArmadillo sparse matrix |
| EMSet | EMSet |
| EMSet-class | Expression and Metadata Set (EMSet) |
| excludeControl | excludeControl |
| filterByControl | filterByControl |
| filterByOutliers | filterByOutliers |
| filterLowAbundanceGenes | filterLowAbundanceGenes |
| func_DESeq | func_DESeq |
| loadCellRanger | loadCellRanger |
| normaliseBatches | normaliseBatches |
| normaliseByRLE | normaliseByRLE |
| plotAverageGeneCount | plotAverageGeneCount |
| plotBatchNormQC | plotBatchNormQC |
| plotControlHist | plotControlHist |
| plotControlPctPerSample | plotControlPctPerSample |
| plotDendrogram | plotDendrogram |
| plotFeatureHist | plotFeatureHist |
| plotGeneNumber | plotGeneNumber |
| plotGeneralQC | plotGeneralQC |
| plotLibsizeBoxplot | plotLibsizeBoxplot |
| plotLibsizeHist | plotLibsizeHist |
| plotLibsizePerSample | plotLibsizePerSample |
| plotMDS | plotMDS |
| plotNormQC | plotNormQC |
| plotPCA | plotPCA |
| plotPCAVariance | plotPCAVariance |
| plotSmoothScatter | plotSmoothScatter |
| plotStability | plotStability |
| plotStabilityDendro | plotStabilityDendro |
| plotTopGenesBoxplot | plotTopGenesBoxplot |
| plotTopGenesPerSample | plotTopGenesPerSample |
| plotTSNE | plotTSNE |
| plotUMAP | plotUMAP |
| plotVariableGenes | plotVariableGenes |
| plotVolcano | plotVolcano |
| progressLog | progressLog |
| raw | Retinal Ganglion Cells (100 THY-1 positive, 100 THY-1... |
| raw_set | Retinal Ganglion Cells (100 THY-1 positive, 100 THY-1... |
| regcounts | regcounts |
| regressConfoundingFactors | regressConfoundingFactors |
| rowInfo | rowInfo |
| runCORE | runCORE |
| runDESeq | runDESeq |
| runDESeq2 | runDESeq2 |
| runDiffExpression | runDiffExpression |
| runPCA | runPCA |
| runTSNE | runTSNE |
| runUMAP | runUMAP |
| scranCellCycle | scranCellCycle |
| scranNormalise | scranNormalise |
| sub-EMSet-ANY-ANY-ANY-method | Subsetter for EMSet |
| subsetCondition | subsetCondition |
| subset-EMSet-ANY-ANY-EMSet-method | Replace entries of EMSet |
| updateObject-EMSet-method | updateObject |
| useVariableGenes | useVariableGenes |
| validateEMSet | validateEMSet |
