Man pages for IMB-Computational-Genomics-Lab/ascend
ascend - Analysis of Single Cell Expression, Normalisation, and Differential expression

addGeneLabeladdGeneLabel
analyzed_setRetinal Ganglion Cells (100 THY-1 positive, 100 THY-1...
ascendascend A package for the quality control and analysis of...
calcGeoMeansDenseCalculate geometric means for dense matrices
calcGeoMeansSparseCalculate geometric means of sparse matrices
calcNormFactorDenseCalculate size factors for dense matrices
calcNormFactorSparseCalculate size factors from sparse matrices
calculateCVcalculateCV
calculateQCcalculateQC
clusterAnalysisclusterAnalysis
colInfocolInfo
controlscontrols
convertconvert
convertGeneIDconvertGeneID
convertSparseConvert R sparse matrix to RcppArmadillo sparse matrix
EMSetEMSet
EMSet-classExpression and Metadata Set (EMSet)
excludeControlexcludeControl
filterByControlfilterByControl
filterByOutliersfilterByOutliers
filterLowAbundanceGenesfilterLowAbundanceGenes
func_DESeqfunc_DESeq
loadCellRangerloadCellRanger
normaliseBatchesnormaliseBatches
normaliseByRLEnormaliseByRLE
plotAverageGeneCountplotAverageGeneCount
plotBatchNormQCplotBatchNormQC
plotControlHistplotControlHist
plotControlPctPerSampleplotControlPctPerSample
plotDendrogramplotDendrogram
plotFeatureHistplotFeatureHist
plotGeneNumberplotGeneNumber
plotGeneralQCplotGeneralQC
plotLibsizeBoxplotplotLibsizeBoxplot
plotLibsizeHistplotLibsizeHist
plotLibsizePerSampleplotLibsizePerSample
plotMDSplotMDS
plotNormQCplotNormQC
plotPCAplotPCA
plotPCAVarianceplotPCAVariance
plotSmoothScatterplotSmoothScatter
plotStabilityplotStability
plotStabilityDendroplotStabilityDendro
plotTopGenesBoxplotplotTopGenesBoxplot
plotTopGenesPerSampleplotTopGenesPerSample
plotTSNEplotTSNE
plotUMAPplotUMAP
plotVariableGenesplotVariableGenes
plotVolcanoplotVolcano
progressLogprogressLog
rawRetinal Ganglion Cells (100 THY-1 positive, 100 THY-1...
raw_setRetinal Ganglion Cells (100 THY-1 positive, 100 THY-1...
regcountsregcounts
regressConfoundingFactorsregressConfoundingFactors
rowInforowInfo
runCORErunCORE
runDESeqrunDESeq
runDESeq2runDESeq2
runDiffExpressionrunDiffExpression
runPCArunPCA
runTSNErunTSNE
runUMAPrunUMAP
scranCellCyclescranCellCycle
scranNormalisescranNormalise
sub-EMSet-ANY-ANY-ANY-methodSubsetter for EMSet
subsetConditionsubsetCondition
subset-EMSet-ANY-ANY-EMSet-methodReplace entries of EMSet
updateObject-EMSet-methodupdateObject
useVariableGenesuseVariableGenes
validateEMSetvalidateEMSet
IMB-Computational-Genomics-Lab/ascend documentation built on June 14, 2019, 12:01 p.m.