Files in dynverse/scaterlegacy
Single-cell analysis toolkit for gene expression data in R
.Rbuildignore
.gitignore
.travis.yml
DESCRIPTION
NAMESPACE
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
appveyor.yml
data/sc_example_cell_info.RData
data/sc_example_counts.RData
inst/CITATION
inst/NEWS.Rd
inst/extdata/reads_1.fastq.gz
inst/extdata/reads_2.fastq.gz
inst/extdata/targets.txt
inst/extdata/transcripts.idx
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/server.R
inst/shiny-app.R
inst/sticker_readme.md
inst/ui.R
inst/www/scater_qc_workflow.png
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/figures/dependencies.png
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
scaterlegacy.Rproj
src/calc_exprs.cpp
src/init.cpp
src/matrix_info.cpp
src/scaterlegacy.h
src/utils.cpp
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
