Files in APackOfTheClones

Visualization of Clonal Expansion for Single Cell Immune Profiles

R/RcppExports.R R/scRepertoire_v2_functions.R R/Main_algo.R R/RunAPOTC.R R/typecheck.R R/ApotcIndexing.R R/ApotcData.R R/colors.R R/showCloneHighlight.R R/APackOfTheClones-package.R R/vizAPOTC.R R/clusters.R R/deprecated_functions.R R/data.R R/insert_legend.R R/get_clone_sizes.R R/cluster_labels.R R/Repulsion.R R/ApotcClonalNetwork.R R/AdjustAPOTC.R R/ggplot2_functions.R R/seurat_command.R R/zzz.R R/plot_API.R R/utils.R R/APOTCPlot.R inst/doc/APackOfTheClones-install.R inst/doc/APackOfTheClones-utils.R inst/doc/APackOfTheClones-utils.Rmd inst/doc/APackOfTheClones-install.Rmd inst/doc/APackOfTheClones.Rmd inst/doc/APackOfTheClones-shared.R inst/doc/APackOfTheClones-runs.R inst/doc/APackOfTheClones-shared.Rmd inst/doc/APackOfTheClones-runs.Rmd inst/doc/APackOfTheClones.R tests/testthat.R tests/spelling.R tests/testthat/test-ApotcIndexing.R tests/testthat/test-ApotcData.R tests/testthat/test-insert_legend.R tests/testthat/test-clusters.R tests/testthat/test-utils.R tests/testthat/test-AdjustAPOTC.R tests/testthat/test-APOTCPlot.R tests/testthat/test-seurat_command.R tests/testthat/test-Repulsion.R tests/testthat/test-typecheck.R tests/testthat/test-noscript-defaultApotcPlot.R tests/testthat/test-Main_algo.R tests/testthat/test-vizAPOTC.R tests/testthat/helper-testFunctions.R tests/testthat/test-RunAPOTC.R tests/testthat/test-plot_API.R tests/testthat/test-showCloneHighlight.R tests/testthat/helper-vdiffr.R tests/testthat/test-colors.R tests/testthat/test-ApotcClonalNetwork.R tests/testthat/test-get_clone_sizes.R tests/testthat/test-deprecated_functions.R tests/testthat/testdata/v0/cluster_lists.R vignettes/APackOfTheClones-utils.Rmd vignettes/APackOfTheClones-install.Rmd vignettes/APackOfTheClones.Rmd vignettes/APackOfTheClones-shared.Rmd vignettes/APackOfTheClones-runs.Rmd vignettes/archive/v0-main.Rmd man/overlayLegend.Rd man/getSharedClones.Rd man/deleteApotcData.Rd man/vizAPOTC.Rd man/integrate_tcr.Rd man/APOTCPlot.Rd man/RunAPOTC.Rd man/clonal_expansion_plot.Rd man/getReductionCentroids.Rd man/APackOfTheClones-package.Rd man/getLastApotcDataId.Rd man/count_clone_sizes.Rd man/combined_pbmc.Rd man/renameApotcRun.Rd man/getApotcDataIds.Rd man/showCloneHighlight.Rd man/containsApotcRun.Rd man/removeLegend.Rd man/countCloneSizes.Rd man/AdjustAPOTC.Rd man/mergeCloneSizes.Rd