Files in RGLab/COMPASS
Combinatorial Polyfunctionality Analysis of Single Cells
.Rbuildignore
.github/issue_template.md
.github/workflows/build.yml
.gitignore
COMPASS.Rproj
DESCRIPTION
NAMESPACE
NEWS
R/COMPASS-data.R
R/COMPASS-discrete.R
R/COMPASS-package.R
R/COMPASS.R
R/COMPASSContainer.R
R/COMPASSResult-methods.R
R/CellCounts.R
R/Combinations.R
R/GatingSetToCOMPASS.R
R/GetThresholdedIntensities.R
R/Posterior.R
R/RcppExports.R
R/Response.R
R/Rhat.R
R/Scores.R
R/SimpleCOMPASS.R
R/TotalCounts.R
R/UniqueCombinations.R
R/check_meta.R
R/cleanup.R
R/commonPlot.R
R/description.R
R/melt_.R
R/merge-COMPASSContainer.R
R/miscellaneous.R
R/pheatmap.R
R/plotMeanGamma-2.R
R/plotMeanGamma.R
R/plotMeanGammaMulti.R
R/shinyCOMPASS.R
R/shinyCOMPASSDeps.R
R/subset-COMPASSContainer.R
R/swap.R
R/transpose_list.R
R/utils.R
R/zzz.R
README.md
TODO.md
cleanup
data/COMPASS.rda
examples/COMPASS_fit.R
examples/GenerateSampleCOMPASSContainer.R
examples/GenerateSampleCOMPASSResult.R
examples/GenerateSampleData.R
examples/GetThresholdedIntensities.R
incubator/COMPASS-simulation.R
incubator/HDF5Functions.R
incubator/Scores.R
incubator/combos_counts.R
inst/extdata/SimpleCOMPASSExample.xlsx
inst/extdata/SimpleCOMPASSExamples.csv
inst/shiny/common_functions.R
inst/shiny/scripts.js
inst/shiny/server.R
inst/shiny/ui.R
inst/shiny/withHelp.R
inst/shiny/www/css/shinySplom.css
inst/shiny/www/css/styles.css
inst/shiny/www/jquery-ui/css/ui-lightness/images/animated-overlay.gif
inst/shiny/www/jquery-ui/css/ui-lightness/images/ui-bg_diagonals-thick_18_b81900_40x40.png
inst/shiny/www/jquery-ui/css/ui-lightness/images/ui-bg_diagonals-thick_20_666666_40x40.png
inst/shiny/www/jquery-ui/css/ui-lightness/images/ui-bg_flat_10_000000_40x100.png
inst/shiny/www/jquery-ui/css/ui-lightness/images/ui-bg_glass_100_f6f6f6_1x400.png
inst/shiny/www/jquery-ui/css/ui-lightness/images/ui-bg_glass_100_fdf5ce_1x400.png
inst/shiny/www/jquery-ui/css/ui-lightness/images/ui-bg_glass_65_ffffff_1x400.png
inst/shiny/www/jquery-ui/css/ui-lightness/images/ui-bg_gloss-wave_35_f6a828_500x100.png
inst/shiny/www/jquery-ui/css/ui-lightness/images/ui-bg_highlight-soft_100_eeeeee_1x100.png
inst/shiny/www/jquery-ui/css/ui-lightness/images/ui-bg_highlight-soft_75_ffe45c_1x100.png
inst/shiny/www/jquery-ui/css/ui-lightness/images/ui-icons_222222_256x240.png
inst/shiny/www/jquery-ui/css/ui-lightness/images/ui-icons_228ef1_256x240.png
inst/shiny/www/jquery-ui/css/ui-lightness/images/ui-icons_ef8c08_256x240.png
inst/shiny/www/jquery-ui/css/ui-lightness/images/ui-icons_ffd27a_256x240.png
inst/shiny/www/jquery-ui/css/ui-lightness/images/ui-icons_ffffff_256x240.png
inst/shiny/www/jquery-ui/css/ui-lightness/jquery-ui-1.10.3.custom.css
inst/shiny/www/jquery-ui/css/ui-lightness/jquery-ui-1.10.3.custom.min.css
inst/shiny/www/jquery-ui/js/jquery-1.9.1.js
inst/shiny/www/jquery-ui/js/jquery-ui-1.10.3.custom.js
inst/shiny/www/jquery-ui/js/jquery-ui-1.10.3.custom.min.js
inst/shiny/www/js/d3.js
inst/shiny/www/js/fancyboxify.js
inst/shiny/www/js/gridsterExtras.js
inst/shiny/www/js/resize.js
inst/shiny/www/js/shinySplom.js
inst/shiny/www/js/tooltips.js
inst/shiny/www/js/updateSubsets.js
inst/shiny/www/multiselect/multiselect.css
inst/shiny/www/multiselect/multiselect.js
inst/shiny/www/opentip/opentip.css
inst/shiny/www/opentip/opentip.js
internal/COMPASS-continuous.R
internal/examples/example-COMPASS-mucovac.R
internal/examples/example-COMPASS.R
man/COMPASS-package.Rd
man/COMPASS.Rd
man/COMPASSContainer-data.Rd
man/COMPASSContainer.Rd
man/COMPASSContainerFromGatingSet.Rd
man/COMPASSDescription.Rd
man/COMPASSMCMCDiagnosis.Rd
man/COMPASSResult-accessors.Rd
man/COMPASSResult-data.Rd
man/COMPASSfitToCountsTable.Rd
man/CellCounts.Rd
man/Combinations.Rd
man/FunctionalityScore.Rd
man/GetThresholdedIntensities.Rd
man/PolyfunctionalityScore.Rd
man/Posterior.Rd
man/Response.Rd
man/SimpleCOMPASS.Rd
man/TotalCellCounts.Rd
man/UniqueCombinations.Rd
man/categories.Rd
man/getCounts.Rd
man/markers.Rd
man/melt_.Rd
man/merge.COMPASSContainer.Rd
man/metadata.Rd
man/pheatmap.Rd
man/plot.COMPASSResult.Rd
man/plot2.Rd
man/plotCOMPASSResultStack.Rd
man/print.COMPASSContainer.Rd
man/print.COMPASSResult.Rd
man/scores.Rd
man/select_compass_pops.Rd
man/shinyCOMPASS.Rd
man/shinyCOMPASSDeps.Rd
man/subset.COMPASSContainer.Rd
man/summary.COMPASSContainer.Rd
man/summary.COMPASSResult.Rd
man/translate_marker_names.Rd
man/transpose_list.Rd
old/pheatmap.R
refactor/for_CC_Exp.R
refactor/init_realdata_Casecontrol.R
refactor/master4model_cpp.R
refactor/master_noPu_Exp.R
refactor/realdata_Casecontrol.R
scratch/computing_cell_counts.R
scratch/digamma_compare.cpp
scratch/gsl_compare.cpp
src/COMPASS_init.c
src/CellCounts.cpp
src/CellCounts_character.cpp
src/Makevars
src/Makevars.win
src/RcppExports.cpp
src/digamma.c
src/mat2vec.c
src/melt_dataframe.c
src/melt_matrix.c
src/samplePuPs.cpp
src/transpose_list.c
src/updatealphas_Exp.cpp
src/updatealphas_Exp_MH.cpp
src/updatealphau.cpp
src/updatealphau_noPu_Exp.cpp
src/updatealphau_noPu_Exp_MH.cpp
src/updatebeta_RW.cpp
src/updategammak_noPu.cpp
src/utils.c
tests/test-all.R
tests/testthat/helper-init.R
tests/testthat/test-COMPASS.R
tests/testthat/test-COMPASSPlot.R
tests/testthat/test-CellCounts.R
tests/testthat/test-FunctionalityScore.R
tests/testthat/test-GatingSet2COMPASS.R
vignettes/COMPASS.Rmd
vignettes/SimpleCOMPASS.Rmd
vignettes/SimpleCOMPASS.pdf
vignettes/bibliography.bib
