Files in scater
Single-Cell Analysis Toolkit for Gene Expression Data in R

NAMESPACE
DESCRIPTION
build/vignette.rds
src/utils.cpp
src/sum_counts.cpp
src/RcppExports.cpp
src/combined_qc.cpp
src/utils.h
R/calculateTPM.R R/retrieveCellInfo.R R/plot_central.R R/multiplot.R R/plotExplanatoryVariables.R R/SCESet-methods.R R/runColDataPCA.R R/utils_reddim.R R/uniquifyFeatureNames.R R/plot_reddim.R R/calculateFPKM.R R/addPerCellQC.R R/ggsce.R R/sumCountsAcrossCells.R R/retrieveFeatureInfo.R R/SingleCellExperiment-methods.R R/AllGenerics.R R/RcppExports.R R/makePerCellDF.R R/numDetectedAcrossCells.R R/utils_plotting.R R/runMultiUMAP.R R/calculateAverage.R R/perFeatureQCMetrics.R R/plotPlatePosition.R R/plotHighestExprs.R R/calculateCPM.R R/normalizeCounts.R R/runPCA.R R/librarySizeFactors.R R/perCellQCMetrics.R R/plot_colours.R R/isOutlier.R R/logNormCounts.R R/runMDS.R R/getVarianceExplained.R R/utils_parallel.R R/nexprs.R R/mockSCE.R R/plotHeatmap.R R/medianSizeFactors.R R/plotRowData.R R/quickPerCellQC.R R/plotScater.R R/AllClasses.R R/runUMAP.R R/runTSNE.R R/plotColData.R R/plotDots.R R/plotExpression.R R/plotRLE.R R/getExplanatoryPCs.R R/plotReducedDim.R R/makePerFeatureDF.R R/plotExplanatoryPCs.R R/namespace.R R/runDiffusionMap.R R/defunct.R R/sumCountsAcrossFeatures.R R/utils_subset.R R/numDetectedAcrossFeatures.R R/runNMF.R R/readSparseCounts.R R/annotateBMFeatures.R vignettes/overview.Rmd man/runMDS.Rd man/sumCountsAcrossFeatures.Rd man/plotScater.Rd man/bootstraps.Rd man/mockSCE.Rd man/toSingleCellExperiment.Rd man/runTSNE.Rd man/SCESet.Rd man/uniquifyFeatureNames.Rd man/isOutlier.Rd man/defunct.Rd man/scater-plot-args.Rd man/makePerCellDF.Rd man/getExplanatoryPCs.Rd man/plotReducedDim.Rd man/plotHeatmap.Rd man/logNormCounts.Rd man/runMultiUMAP.Rd man/calculateCPM.Rd man/perCellQCMetrics.Rd man/plot_reddim.Rd man/sumCountsAcrossCells.Rd man/plotRLE.Rd man/plotExpression.Rd man/getVarianceExplained.Rd man/numDetectedAcrossCells.Rd man/librarySizeFactors.Rd man/quickPerCellQC.Rd man/readSparseCounts.Rd man/normalizeCounts.Rd man/retrieveCellInfo.Rd man/runDiffusionMap.Rd man/plotRowData.Rd man/accessors.Rd man/calculateFPKM.Rd man/runUMAP.Rd man/numDetectedAcrossFeatures.Rd man/scater-utils.Rd man/plotHighestExprs.Rd man/addPerCellQC.Rd man/plotPlatePosition.Rd man/medianSizeFactors.Rd man/ggsce.Rd man/makePerFeatureDF.Rd man/plotExplanatoryVariables.Rd man/plotColData.Rd man/plotExplanatoryPCs.Rd man/retrieveFeatureInfo.Rd man/annotateBMFeatures.Rd man/calculateTPM.Rd man/runNMF.Rd man/runColDataPCA.Rd man/calculateAverage.Rd man/plotDots.Rd man/runPCA.Rd man/nexprs.Rd man/multiplot.Rd man/perFeatureQCMetrics.Rd tests/testthat.R tests/testthat/test-plot-exprs.R tests/testthat/test-plot-utils.R tests/testthat/test-sum-across-feat.R tests/testthat/test-qc-calc.R tests/testthat/test-norm.R tests/testthat/test-plot-dimred.R tests/testthat/test-qc-outlier.R tests/testthat/test-red-dim.R tests/testthat/test-sum-across-cells.R tests/testthat/test-calc-ave.R tests/testthat/test-utils.R tests/testthat/test-plot-scater.R tests/testthat/test-plot-other.R tests/testthat/test-calc-cpm.R tests/testthat/test-nexprs.R tests/testthat/test-expl-var.R tests/testthat/setup.R tests/testthat/test-feat-proc.R tests/testthat/test-load-data.R tests/testthat/test-SingleCellExperiment-methods.R tests/testthat/test-qc-plot.R
inst/NEWS.Rd
inst/CITATION
inst/doc/overview.html
inst/doc/overview.Rmd inst/doc/overview.R
inst/www/scater_qc_workflow.png
scater documentation built on June 28, 2020, 2 a.m.