├── .Rbuildignore ├── .github └── workflows │ ├── R-CMD-check.yml │ └── vignette.yml ├── .gitignore ├── DESCRIPTION ├── LICENSE ├── NAMESPACE ├── NEWS.md ├── R ├── check.R ├── constructMarkovChain.R ├── dandelionR.R ├── data.R ├── determMultiscaleSpace.R ├── differentiationProbabilities.R ├── filterCells.R ├── getPbs.R ├── markovProbability.R ├── maxMinSampling.R ├── miloUmap.R ├── minMaxScale.R ├── projectProbability.R ├── projectPseudotimeToCell.R ├── setupVdjPseudobulk.R ├── splitCTgene.R ├── terminalStateFromMarkovChain.R └── vdjPseudobulk.R ├── README.md ├── _pkgdown.yml ├── data ├── demo_airr.rda ├── demo_sce.rda └── sce_vdj.rda ├── inst └── CITATION ├── man ├── chainAssign.Rd ├── dandelionR.Rd ├── demo_airr.Rd ├── demo_sce.Rd ├── differentiationProbabilities.Rd ├── dot-KNNind.Rd ├── dot-RANNinx.Rd ├── dot-addColData.Rd ├── dot-allowedChain.Rd ├── dot-calDif.Rd ├── dot-classCheck.Rd ├── dot-collapse_nested_list.Rd ├── dot-constructMarkovChain.Rd ├── dot-determExtractColN.Rd ├── dot-determTerminal.Rd ├── dot-determineMultiscaleSpace.Rd ├── dot-extractVdj.Rd ├── dot-featureSpaceConstruct.Rd ├── dot-filterCells.Rd ├── dot-filterProductivity.Rd ├── dot-filterUnmapped.Rd ├── dot-findNewWaypoints.Rd ├── dot-generateExtractColumn.Rd ├── dot-generateExtractName.Rd ├── dot-getPbs.Rd ├── dot-getPbsCol.Rd ├── dot-getPbsPerCol.Rd ├── dot-maxMinSampling.Rd ├── dot-minMaxScale.Rd ├── dot-normalizeFeatureSpace.Rd ├── dot-normalizePerVDJ.Rd ├── dot-packFeatureSpace.Rd ├── dot-removeEdge.Rd ├── dot-subsetSce.Rd ├── dot-terminalStateFromMarkovChain.Rd ├── dot-typeCheck.Rd ├── dot-waypiontsPerCol.Rd ├── formatVdj.Rd ├── markovProbability.Rd ├── miloUmap.Rd ├── projectProbability.Rd ├── projectPseudotimeToCell.Rd ├── project_single_value.Rd ├── sce_vdj.Rd ├── setupVdjPseudobulk.Rd ├── splitCTgene.Rd └── vdjPseudobulk.Rd ├── tests ├── testthat.R └── testthat │ ├── test-check.R │ ├── test-filterCells.R │ ├── test-fromscRepertoire.R │ ├── test-getPbs.R │ ├── test-markovProbability.R │ ├── test-miloUmap.R │ ├── test-minMaxScale.R │ ├── test-projectPseudotimeToCell.R │ ├── test-setupVdjPseudobulk.R │ └── test-vdjPseudobulk.R └── vignettes ├── dandelionR.Rmd ├── dandelionR_with_slingshot.Rmd └── vignette_reproduce_original.rmd /.Rbuildignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tuonglab/dandelionR/HEAD/.Rbuildignore -------------------------------------------------------------------------------- /.github/workflows/R-CMD-check.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tuonglab/dandelionR/HEAD/.github/workflows/R-CMD-check.yml -------------------------------------------------------------------------------- /.github/workflows/vignette.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tuonglab/dandelionR/HEAD/.github/workflows/vignette.yml -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tuonglab/dandelionR/HEAD/.gitignore -------------------------------------------------------------------------------- /DESCRIPTION: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tuonglab/dandelionR/HEAD/DESCRIPTION -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 1 | YEAR: 2024 2 | COPYRIGHT HOLDER: Jiawei Yu and Zewen Kelvin Tuong -------------------------------------------------------------------------------- /NAMESPACE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tuonglab/dandelionR/HEAD/NAMESPACE -------------------------------------------------------------------------------- /NEWS.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tuonglab/dandelionR/HEAD/NEWS.md -------------------------------------------------------------------------------- /R/check.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tuonglab/dandelionR/HEAD/R/check.R -------------------------------------------------------------------------------- /R/constructMarkovChain.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tuonglab/dandelionR/HEAD/R/constructMarkovChain.R -------------------------------------------------------------------------------- /R/dandelionR.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tuonglab/dandelionR/HEAD/R/dandelionR.R -------------------------------------------------------------------------------- /R/data.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tuonglab/dandelionR/HEAD/R/data.R -------------------------------------------------------------------------------- /R/determMultiscaleSpace.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tuonglab/dandelionR/HEAD/R/determMultiscaleSpace.R -------------------------------------------------------------------------------- /R/differentiationProbabilities.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tuonglab/dandelionR/HEAD/R/differentiationProbabilities.R -------------------------------------------------------------------------------- /R/filterCells.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tuonglab/dandelionR/HEAD/R/filterCells.R -------------------------------------------------------------------------------- /R/getPbs.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tuonglab/dandelionR/HEAD/R/getPbs.R -------------------------------------------------------------------------------- /R/markovProbability.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tuonglab/dandelionR/HEAD/R/markovProbability.R -------------------------------------------------------------------------------- /R/maxMinSampling.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tuonglab/dandelionR/HEAD/R/maxMinSampling.R -------------------------------------------------------------------------------- /R/miloUmap.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tuonglab/dandelionR/HEAD/R/miloUmap.R -------------------------------------------------------------------------------- /R/minMaxScale.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tuonglab/dandelionR/HEAD/R/minMaxScale.R -------------------------------------------------------------------------------- /R/projectProbability.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tuonglab/dandelionR/HEAD/R/projectProbability.R -------------------------------------------------------------------------------- /R/projectPseudotimeToCell.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tuonglab/dandelionR/HEAD/R/projectPseudotimeToCell.R -------------------------------------------------------------------------------- /R/setupVdjPseudobulk.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tuonglab/dandelionR/HEAD/R/setupVdjPseudobulk.R -------------------------------------------------------------------------------- /R/splitCTgene.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tuonglab/dandelionR/HEAD/R/splitCTgene.R -------------------------------------------------------------------------------- /R/terminalStateFromMarkovChain.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tuonglab/dandelionR/HEAD/R/terminalStateFromMarkovChain.R -------------------------------------------------------------------------------- /R/vdjPseudobulk.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tuonglab/dandelionR/HEAD/R/vdjPseudobulk.R -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tuonglab/dandelionR/HEAD/README.md -------------------------------------------------------------------------------- /_pkgdown.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tuonglab/dandelionR/HEAD/_pkgdown.yml -------------------------------------------------------------------------------- /data/demo_airr.rda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tuonglab/dandelionR/HEAD/data/demo_airr.rda -------------------------------------------------------------------------------- /data/demo_sce.rda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tuonglab/dandelionR/HEAD/data/demo_sce.rda -------------------------------------------------------------------------------- /data/sce_vdj.rda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tuonglab/dandelionR/HEAD/data/sce_vdj.rda -------------------------------------------------------------------------------- /inst/CITATION: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tuonglab/dandelionR/HEAD/inst/CITATION -------------------------------------------------------------------------------- /man/chainAssign.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tuonglab/dandelionR/HEAD/man/chainAssign.Rd -------------------------------------------------------------------------------- /man/dandelionR.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tuonglab/dandelionR/HEAD/man/dandelionR.Rd -------------------------------------------------------------------------------- /man/demo_airr.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tuonglab/dandelionR/HEAD/man/demo_airr.Rd -------------------------------------------------------------------------------- /man/demo_sce.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tuonglab/dandelionR/HEAD/man/demo_sce.Rd -------------------------------------------------------------------------------- /man/differentiationProbabilities.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tuonglab/dandelionR/HEAD/man/differentiationProbabilities.Rd -------------------------------------------------------------------------------- /man/dot-KNNind.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tuonglab/dandelionR/HEAD/man/dot-KNNind.Rd -------------------------------------------------------------------------------- /man/dot-RANNinx.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tuonglab/dandelionR/HEAD/man/dot-RANNinx.Rd -------------------------------------------------------------------------------- /man/dot-addColData.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tuonglab/dandelionR/HEAD/man/dot-addColData.Rd -------------------------------------------------------------------------------- /man/dot-allowedChain.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tuonglab/dandelionR/HEAD/man/dot-allowedChain.Rd -------------------------------------------------------------------------------- /man/dot-calDif.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tuonglab/dandelionR/HEAD/man/dot-calDif.Rd -------------------------------------------------------------------------------- /man/dot-classCheck.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tuonglab/dandelionR/HEAD/man/dot-classCheck.Rd -------------------------------------------------------------------------------- /man/dot-collapse_nested_list.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tuonglab/dandelionR/HEAD/man/dot-collapse_nested_list.Rd -------------------------------------------------------------------------------- /man/dot-constructMarkovChain.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tuonglab/dandelionR/HEAD/man/dot-constructMarkovChain.Rd -------------------------------------------------------------------------------- /man/dot-determExtractColN.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tuonglab/dandelionR/HEAD/man/dot-determExtractColN.Rd -------------------------------------------------------------------------------- /man/dot-determTerminal.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tuonglab/dandelionR/HEAD/man/dot-determTerminal.Rd -------------------------------------------------------------------------------- /man/dot-determineMultiscaleSpace.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tuonglab/dandelionR/HEAD/man/dot-determineMultiscaleSpace.Rd -------------------------------------------------------------------------------- /man/dot-extractVdj.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tuonglab/dandelionR/HEAD/man/dot-extractVdj.Rd -------------------------------------------------------------------------------- /man/dot-featureSpaceConstruct.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tuonglab/dandelionR/HEAD/man/dot-featureSpaceConstruct.Rd -------------------------------------------------------------------------------- /man/dot-filterCells.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tuonglab/dandelionR/HEAD/man/dot-filterCells.Rd -------------------------------------------------------------------------------- /man/dot-filterProductivity.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tuonglab/dandelionR/HEAD/man/dot-filterProductivity.Rd -------------------------------------------------------------------------------- /man/dot-filterUnmapped.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tuonglab/dandelionR/HEAD/man/dot-filterUnmapped.Rd -------------------------------------------------------------------------------- /man/dot-findNewWaypoints.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tuonglab/dandelionR/HEAD/man/dot-findNewWaypoints.Rd -------------------------------------------------------------------------------- /man/dot-generateExtractColumn.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tuonglab/dandelionR/HEAD/man/dot-generateExtractColumn.Rd -------------------------------------------------------------------------------- /man/dot-generateExtractName.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tuonglab/dandelionR/HEAD/man/dot-generateExtractName.Rd -------------------------------------------------------------------------------- /man/dot-getPbs.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tuonglab/dandelionR/HEAD/man/dot-getPbs.Rd -------------------------------------------------------------------------------- /man/dot-getPbsCol.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tuonglab/dandelionR/HEAD/man/dot-getPbsCol.Rd -------------------------------------------------------------------------------- /man/dot-getPbsPerCol.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tuonglab/dandelionR/HEAD/man/dot-getPbsPerCol.Rd -------------------------------------------------------------------------------- /man/dot-maxMinSampling.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tuonglab/dandelionR/HEAD/man/dot-maxMinSampling.Rd -------------------------------------------------------------------------------- /man/dot-minMaxScale.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tuonglab/dandelionR/HEAD/man/dot-minMaxScale.Rd -------------------------------------------------------------------------------- /man/dot-normalizeFeatureSpace.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tuonglab/dandelionR/HEAD/man/dot-normalizeFeatureSpace.Rd -------------------------------------------------------------------------------- /man/dot-normalizePerVDJ.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tuonglab/dandelionR/HEAD/man/dot-normalizePerVDJ.Rd -------------------------------------------------------------------------------- /man/dot-packFeatureSpace.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tuonglab/dandelionR/HEAD/man/dot-packFeatureSpace.Rd -------------------------------------------------------------------------------- /man/dot-removeEdge.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tuonglab/dandelionR/HEAD/man/dot-removeEdge.Rd -------------------------------------------------------------------------------- /man/dot-subsetSce.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tuonglab/dandelionR/HEAD/man/dot-subsetSce.Rd -------------------------------------------------------------------------------- /man/dot-terminalStateFromMarkovChain.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tuonglab/dandelionR/HEAD/man/dot-terminalStateFromMarkovChain.Rd -------------------------------------------------------------------------------- /man/dot-typeCheck.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tuonglab/dandelionR/HEAD/man/dot-typeCheck.Rd -------------------------------------------------------------------------------- /man/dot-waypiontsPerCol.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tuonglab/dandelionR/HEAD/man/dot-waypiontsPerCol.Rd -------------------------------------------------------------------------------- /man/formatVdj.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tuonglab/dandelionR/HEAD/man/formatVdj.Rd -------------------------------------------------------------------------------- /man/markovProbability.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tuonglab/dandelionR/HEAD/man/markovProbability.Rd -------------------------------------------------------------------------------- /man/miloUmap.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tuonglab/dandelionR/HEAD/man/miloUmap.Rd -------------------------------------------------------------------------------- /man/projectProbability.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tuonglab/dandelionR/HEAD/man/projectProbability.Rd -------------------------------------------------------------------------------- /man/projectPseudotimeToCell.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tuonglab/dandelionR/HEAD/man/projectPseudotimeToCell.Rd -------------------------------------------------------------------------------- /man/project_single_value.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tuonglab/dandelionR/HEAD/man/project_single_value.Rd -------------------------------------------------------------------------------- /man/sce_vdj.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tuonglab/dandelionR/HEAD/man/sce_vdj.Rd -------------------------------------------------------------------------------- /man/setupVdjPseudobulk.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tuonglab/dandelionR/HEAD/man/setupVdjPseudobulk.Rd -------------------------------------------------------------------------------- /man/splitCTgene.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tuonglab/dandelionR/HEAD/man/splitCTgene.Rd -------------------------------------------------------------------------------- /man/vdjPseudobulk.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tuonglab/dandelionR/HEAD/man/vdjPseudobulk.Rd -------------------------------------------------------------------------------- /tests/testthat.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tuonglab/dandelionR/HEAD/tests/testthat.R -------------------------------------------------------------------------------- /tests/testthat/test-check.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tuonglab/dandelionR/HEAD/tests/testthat/test-check.R -------------------------------------------------------------------------------- /tests/testthat/test-filterCells.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tuonglab/dandelionR/HEAD/tests/testthat/test-filterCells.R -------------------------------------------------------------------------------- /tests/testthat/test-fromscRepertoire.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tuonglab/dandelionR/HEAD/tests/testthat/test-fromscRepertoire.R -------------------------------------------------------------------------------- /tests/testthat/test-getPbs.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tuonglab/dandelionR/HEAD/tests/testthat/test-getPbs.R -------------------------------------------------------------------------------- /tests/testthat/test-markovProbability.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tuonglab/dandelionR/HEAD/tests/testthat/test-markovProbability.R -------------------------------------------------------------------------------- /tests/testthat/test-miloUmap.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tuonglab/dandelionR/HEAD/tests/testthat/test-miloUmap.R -------------------------------------------------------------------------------- /tests/testthat/test-minMaxScale.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tuonglab/dandelionR/HEAD/tests/testthat/test-minMaxScale.R -------------------------------------------------------------------------------- /tests/testthat/test-projectPseudotimeToCell.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tuonglab/dandelionR/HEAD/tests/testthat/test-projectPseudotimeToCell.R -------------------------------------------------------------------------------- /tests/testthat/test-setupVdjPseudobulk.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tuonglab/dandelionR/HEAD/tests/testthat/test-setupVdjPseudobulk.R -------------------------------------------------------------------------------- /tests/testthat/test-vdjPseudobulk.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tuonglab/dandelionR/HEAD/tests/testthat/test-vdjPseudobulk.R -------------------------------------------------------------------------------- /vignettes/dandelionR.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tuonglab/dandelionR/HEAD/vignettes/dandelionR.Rmd -------------------------------------------------------------------------------- /vignettes/dandelionR_with_slingshot.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tuonglab/dandelionR/HEAD/vignettes/dandelionR_with_slingshot.Rmd -------------------------------------------------------------------------------- /vignettes/vignette_reproduce_original.rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tuonglab/dandelionR/HEAD/vignettes/vignette_reproduce_original.rmd --------------------------------------------------------------------------------