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

.Rbuildignore
.gitignore
.travis.yml
DESCRIPTION
NAMESPACE
R/AllClasses.R R/AllGenerics.R R/SCESet-methods.R R/SingleCellExperiment-methods.R R/calculateAverage.R R/calculateCPM.R R/calculateFPKM.R R/calculateQCMetrics.R R/calculateTPM.R R/centreSizeFactors.R R/getBMFeatureAnnos.R R/getExplanatoryPCs.R R/getVarianceExplained.R R/isOutlier.R R/librarySizeFactors.R R/multiplot.R R/nexprs.R R/normalizeCounts.R R/normalizeSCE.R R/plotExplanatoryPCs.R R/plotExplanatoryVariables.R R/plotExpression.R R/plotExprsFreqVsMean.R R/plotExprsVsTxLength.R R/plotHeatmap.R R/plotHighestExprs.R R/plotPlatePosition.R R/plotRLE.R R/plotReducedDim.R R/plotScater.R R/plot_central.R R/plot_colours.R R/plot_metadata.R R/plot_reddim.R R/plot_utils.R R/readSparseCounts.R R/runDiffusionMap.R R/runMDS.R R/runPCA.R R/runTSNE.R R/runUMAP.R R/sc_example_cell_info-data.R R/sc_example_counts-data.R R/scater-package.R R/sumCountsAcrossFeatures.R R/uniquifyFeatureNames.R R/utils_parallel.R R/utils_qc_hunter.R R/utils_sizeFactors.R R/utils_subset.R R/verbs.R README.md
appveyor.yml
data/sc_example_cell_info.RData
data/sc_example_counts.RData
inst/CITATION
inst/NEWS.Rd
inst/scater_qc_workflow.graffle
inst/scater_qc_workflow.png
inst/scater_sticker.svg
inst/scater_sticker_300dpi.pdf
inst/scater_sticker_300dpi.png
inst/scater_sticker_small.png
inst/scater_sticker_web.pdf inst/sticker_readme.md
inst/www/scater_qc_workflow.png
man/SCESet.Rd man/accessors.Rd man/arrange.Rd man/bootstraps.Rd man/calculateAverage.Rd man/calculateCPM.Rd man/calculateFPKM.Rd man/calculateQCMetrics.Rd man/calculateTPM.Rd man/centreSizeFactors.Rd man/filter.Rd man/getBMFeatureAnnos.Rd man/getExplanatoryPCs.Rd man/getVarianceExplained.Rd man/isOutlier.Rd man/librarySizeFactors.Rd man/multiplot.Rd man/mutate.Rd man/nexprs.Rd man/normalize.Rd man/normalizeCounts.Rd man/plotColData.Rd man/plotExplanatoryPCs.Rd man/plotExplanatoryVariables.Rd man/plotExpression.Rd man/plotExprsFreqVsMean.Rd man/plotExprsVsTxLength.Rd man/plotHeatmap.Rd man/plotHighestExprs.Rd man/plotPlatePosition.Rd man/plotRLE.Rd man/plotReducedDim.Rd man/plotRowData.Rd man/plotScater.Rd man/plot_reddim.Rd man/readSparseCounts.Rd man/rename.Rd man/runDiffusionMap.Rd man/runMDS.Rd man/runPCA.Rd man/runTSNE.Rd man/runUMAP.Rd man/sc_example_cell_info.Rd man/sc_example_counts.Rd man/scater-package.Rd man/scater-plot-args.Rd man/scater-vis-var.Rd man/sumCountsAcrossFeatures.Rd man/toSingleCellExperiment.Rd man/uniquifyFeatureNames.Rd
src/Makevars
src/Makevars.win
src/calc_exprs.cpp
src/combined_qc.cpp
src/init.cpp
src/num_exprs.cpp
src/scater.h
src/sum_counts.cpp
src/utils.cpp
src/utils.h
tests/testthat.R tests/testthat/setup-sce.R tests/testthat/test-SingleCellExperiment-methods.R tests/testthat/test-calc-ave.R tests/testthat/test-calc-cpm.R tests/testthat/test-calc-nexprs.R tests/testthat/test-expl-var.R tests/testthat/test-feat-proc.R tests/testthat/test-load-data.R tests/testthat/test-norm.R tests/testthat/test-plot-dimred.R tests/testthat/test-plot-exprs.R tests/testthat/test-plot-other.R tests/testthat/test-plot-scater.R tests/testthat/test-plot-utils.R tests/testthat/test-qc-calc.R tests/testthat/test-qc-outlier.R tests/testthat/test-qc-plot.R tests/testthat/test-red-dim.R tests/testthat/test-verbs.R vignettes/vignette-dataviz.Rmd vignettes/vignette-intro.Rmd vignettes/vignette-qc.Rmd
davismcc/scater documentation built on Nov. 29, 2018, 5:27 a.m.