Files in dynverse/scaterlegacy

Single-cell analysis toolkit for gene expression data in R

R/10ximport-wrapper.R R/AllClasses.R R/AllGenerics.R R/SCESet-methods.R R/calculate-expression.R R/cxx_utils.R R/feature-preprocessing.R R/gui.R R/kallisto-wrapper.R R/magic.R R/normalisation.R R/plotting.R R/qc.R R/salmon-wrapper.R R/sc_example_cell_info-data.R R/sc_example_counts-data.R R/scater-package.R R/test.R R/tximport-wrapper.R R/utils.R R/verbs.R README.md inst/scater_sticker_300dpi.pdf inst/scater_sticker_web.pdf inst/server.R inst/shiny-app.R inst/sticker_readme.md inst/ui.R man/SCESet-subset.Rd man/SCESet.Rd man/areSizeFactorsCentred.Rd man/arrange.Rd man/bootstraps.Rd man/calcAverage.Rd man/calcIsExprs.Rd man/calculateCPM.Rd man/calculateFPKM.Rd man/calculateQCMetrics.Rd man/calculateTPM.Rd man/cellNames.Rd man/cellPairwiseDistances.Rd man/counts.Rd man/cpm.Rd man/fData.Rd man/featureControlInfo.Rd man/featurePairwiseDistances.Rd man/filter.Rd man/findImportantPCs.Rd man/fpkm.Rd man/fromCellDataSet.Rd man/getBMFeatureAnnos.Rd man/getExprs.Rd man/get_exprs.Rd man/isOutlier.Rd man/isSpike.Rd man/is_exprs.Rd man/mergeSCESet.Rd man/multiplot.Rd man/mutate.Rd man/newSCESet.Rd man/nexprs.Rd man/norm_counts.Rd man/norm_cpm.Rd man/norm_exprs.Rd man/norm_fpkm.Rd man/norm_tpm.Rd man/normaliseExprs.Rd man/normalize.Rd man/pData.Rd man/plot.Rd man/plotDiffusionMap.Rd man/plotExplanatoryVariables.Rd man/plotExpression.Rd man/plotExprsFreqVsMean.Rd man/plotExprsVsTxLength.Rd man/plotFeatureData.Rd man/plotHighestExprs.Rd man/plotMDS.Rd man/plotMetadata.Rd man/plotPCA.Rd man/plotPhenoData.Rd man/plotPlatePosition.Rd man/plotQC.Rd man/plotRLE.Rd man/plotReducedDim.Rd man/plotTSNE.Rd man/read10XResults.Rd man/readKallistoResults.Rd man/readKallistoResultsOneSample.Rd man/readSalmonResults.Rd man/readSalmonResultsOneSample.Rd man/readTxResults.Rd man/reducedDimension.Rd man/rename.Rd man/runKallisto.Rd man/runSalmon.Rd man/sc_example_cell_info.Rd man/sc_example_counts.Rd man/scater_gui.Rd man/scaterlegacy-package.Rd man/setSpike.Rd man/set_exprs.Rd man/sizeFactors.Rd man/spikes.Rd man/stand_exprs.Rd man/summariseExprsAcrossFeatures.Rd man/toCellDataSet.Rd man/tpm.Rd man/updateSCESet.Rd man/whichSpike.Rd man/writeSCESet.Rd tests/testthat.R tests/testthat/test-SCESet-methods.R tests/testthat/test-calculate-expression.R tests/testthat/test-classes.R tests/testthat/test-feature-preprocessing.R tests/testthat/test-kallisto-wrapper.R tests/testthat/test-magic.R tests/testthat/test-normalisation.R tests/testthat/test-plotting.R tests/testthat/test-qc.R tests/testthat/test-summariseExprsAcrossFeatures.R tests/testthat/test-tximport-wrapper.R tests/testthat/test-verbs.R vignettes/vignette.Rmd