├── .Rbuildignore ├── .github ├── ISSUE_TEMPLATE │ ├── bug_report.md │ ├── feature-requests.md │ └── other-issues.md └── workflows │ └── RCmdCheck.yaml ├── .gitignore ├── DESCRIPTION ├── LICENSE ├── NAMESPACE ├── NEWS ├── R ├── AllGenerics.R ├── associationTest.R ├── cascade.R ├── clusterExpressionPatterns.R ├── conditionTest.R ├── data.R ├── diffEndTest.R ├── earlyDETest.R ├── evaluateK.R ├── fitGAM.R ├── getSmootherPvalues.R ├── getSmootherTestStats.R ├── nknots.R ├── patternTest.R ├── plotGeneCount.R ├── plotSmoothers.R ├── predictCells.R ├── predictSmooth.R ├── startVsEndTest.R └── utils.R ├── README.md ├── _pkgdown.yml ├── codecov.yml ├── data ├── celltype.rda ├── countMatrix.rda ├── crv.rda ├── gamList.rda └── sds.rda ├── inst └── CITATION ├── man ├── associationTest.Rd ├── cascade.Rd ├── celltype.Rd ├── clusterExpressionPatterns.Rd ├── conditionTest.Rd ├── countMatrix.Rd ├── crv.Rd ├── diffEndTest.Rd ├── earlyDETest.Rd ├── evaluateK.Rd ├── fitGAM.Rd ├── gamList.Rd ├── getSmootherPvalues.Rd ├── getSmootherTestStats.Rd ├── nknots.Rd ├── patternTest.Rd ├── plotGeneCount.Rd ├── plotSmoothers.Rd ├── plot_evalutateK_results.Rd ├── predictCells.Rd ├── predictSmooth.Rd ├── sds.Rd └── startVsEndTest.Rd ├── tests ├── testthat.R └── testthat │ ├── Rplots.pdf │ ├── testConditions.R │ ├── testConsistentOutput.R │ ├── testDETestDetails.R │ ├── testFailures.R │ ├── testFoldChanges.R │ ├── testOneLineage.R │ ├── testPlots.R │ ├── testPredict.R │ └── testThreeLineages.R └── vignettes ├── Monocle.Rmd ├── cellRankVignette.Rmd ├── cellRankVignette.html ├── cheatsheet_highRes.jpeg ├── evalK_paul.png ├── fitGAM.Rmd ├── multipleConditions.Rmd ├── tradeSeq.Rmd └── tradeSeq.bib /.Rbuildignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/statOmics/tradeSeq/HEAD/.Rbuildignore -------------------------------------------------------------------------------- /.github/ISSUE_TEMPLATE/bug_report.md: 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