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