├── .RBuildginore ├── .RData ├── .Rapp.history ├── .Rbuildignore ├── .gitignore ├── DESCRIPTION ├── NAMESPACE ├── NEWS ├── R ├── RcppExports.R ├── ascend.R ├── ascend_DESeq.R ├── ascend_DESeq2.R ├── ascend_cellranger.R ├── ascend_clustering.R ├── ascend_confoundingfactors.R ├── ascend_diffexpression.R ├── ascend_dimreduction.R ├── ascend_filtering.R ├── ascend_getters.R ├── ascend_imports.R ├── ascend_methods.R ├── ascend_normalisation.R ├── ascend_objects.R ├── ascend_plots.R ├── ascend_scran.R ├── ascend_setters.R ├── ascend_subsetters.R ├── ascend_utilities.R ├── data.R └── sysdata.rda ├── README.md ├── ascend.Rproj ├── ascend_banner.png ├── data ├── analyzed_set.rda ├── raw.rda └── raw_set.rda ├── inst └── NEWS ├── man ├── EMSet-class.Rd ├── EMSet.Rd ├── addGeneLabel.Rd ├── analyzed_set.Rd ├── ascend.Rd ├── calcGeoMeansDense.Rd ├── calcGeoMeansSparse.Rd ├── calcNormFactorDense.Rd ├── calcNormFactorSparse.Rd ├── calculateCV.Rd ├── calculateQC.Rd ├── clusterAnalysis.Rd ├── colInfo.Rd ├── controls.Rd ├── convert.Rd ├── convertGeneID.Rd ├── convertSparse.Rd ├── excludeControl.Rd ├── filterByControl.Rd ├── filterByOutliers.Rd ├── filterLowAbundanceGenes.Rd ├── func_DESeq.Rd ├── loadCellRanger.Rd ├── normaliseBatches.Rd ├── normaliseByRLE.Rd ├── plotAverageGeneCount.Rd ├── plotBatchNormQC.Rd ├── plotControlHist.Rd ├── plotControlPctPerSample.Rd ├── plotDendrogram.Rd ├── plotFeatureHist.Rd ├── plotGeneNumber.Rd ├── plotGeneralQC.Rd ├── plotLibsizeBoxplot.Rd ├── plotLibsizeHist.Rd ├── plotLibsizePerSample.Rd ├── plotMDS.Rd ├── plotNormQC.Rd ├── plotPCA.Rd ├── plotPCAVariance.Rd ├── plotSmoothScatter.Rd ├── plotStability.Rd ├── plotStabilityDendro.Rd ├── plotTSNE.Rd ├── plotTopGenesBoxplot.Rd ├── plotTopGenesPerSample.Rd ├── plotUMAP.Rd ├── plotVariableGenes.Rd ├── plotVolcano.Rd ├── progressLog.Rd ├── raw.Rd ├── raw_set.Rd ├── regcounts.Rd ├── regressConfoundingFactors.Rd ├── rowInfo.Rd ├── runCORE.Rd ├── runDESeq.Rd ├── runDESeq2.Rd ├── runDiffExpression.Rd ├── runPCA.Rd ├── runTSNE.Rd ├── runUMAP.Rd ├── scranCellCycle.Rd ├── scranNormalise.Rd ├── sub-EMSet-ANY-ANY-ANY-method.Rd ├── subset-EMSet-ANY-ANY-EMSet-method.Rd ├── subsetCondition.Rd ├── updateObject-EMSet-method.Rd ├── useVariableGenes.Rd └── validateEMSet.Rd ├── src ├── .gitignore ├── Makevars ├── Makevars.win ├── RcppExports.cpp ├── dense_rle.cpp └── sparse_rle.cpp ├── tests ├── testthat.R └── testthat │ ├── test-methods.R │ ├── test-object.R │ └── test-subsetters.R ├── vignettes ├── ascend-installation.Rmd └── ascend-tutorial.Rmd └── workflow.png /.RBuildginore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/IMB-Computational-Genomics-Lab/ascend/HEAD/.RBuildginore -------------------------------------------------------------------------------- /.RData: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/IMB-Computational-Genomics-Lab/ascend/HEAD/.RData 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