COMPASS: Combinatorial Polyfunctionality Analysis of Single Cells

COMPASS is a statistical framework that enables unbiased analysis of antigen-specific T-cell subsets. COMPASS uses a Bayesian hierarchical framework to model all observed cell-subsets and select the most likely to be antigen-specific while regularizing the small cell counts that often arise in multi-parameter space. The model provides a posterior probability of specificity for each cell subset and each sample, which can be used to profile a subject's immune response to external stimuli such as infection or vaccination.

AuthorLynn Lin, Kevin Ushey, Greg Finak, Ravio Kolde (pheatmap)
Date of publicationNone
MaintainerGreg Finak <gfinak@fhcrc.org>
LicenseArtistic-2.0
Version1.12.0

View on Bioconductor

Man pages

categories: Categories

CellCounts: Compute Number of Cells Positive for Certain Cytokine...

Combinations: Generate Combinations

COMPASS: Fit the COMPASS Model

COMPASSContainer: Generate the Data Object used by COMPASS

COMPASSContainer-data: Simulated COMPASSContainer

COMPASSContainerFromGatingSet: Create a COMPASS Container from a GatingSet

COMPASSDescription: Get and Set the Description for the Shiny Application

COMPASS-package: COMPASS (Combinatorial Polyfunctionality Analysis of...

COMPASSResult-accessors: COMPASSResult Accessors

COMPASSResult-data: Simulated COMPASS fit

FunctionalityScore: Compute the Functionality Score for each subject fit in a...

GetThresholdedIntensities: Extract Thresholded Intensities from a GatingSet

markers: Markers

melt_: Make a 'Wide' data set 'Long'

merge.COMPASSContainer: Merge Two COMPASSContainers

metadata: Metadata

pheatmap: A function to draw clustered heatmaps.

plot2: Plot a pair of COMPASSResults

plot.COMPASSResult: Plot a COMPASSResult

PolyfunctionalityScore: Compute the Polyfunctionality Score for each subject fit in a...

Posterior: Retrieve Posterior Measures from a COMPASS fit

print.COMPASSContainer: Print a COMPASSContainer Object

print.COMPASSResult: Print a COMPASSResult Object

scores: Fetch the table of scores and metadata from a COMPASSResult...

shinyCOMPASS: Start a Shiny Application for Visualizing COMPASS Results

shinyCOMPASSDeps: List Shiny Dependencies

SimpleCOMPASS: Fit the discrete COMPASS Model

subset.COMPASSContainer: Subset a COMPASSContainer

summary.COMPASSContainer: Summarize a COMPASSContainer Object

summary.COMPASSResult: Summarize a COMPASSResult Object

TotalCellCounts: Compute Total Cell Counts

transpose_list: Transpose a List

UniqueCombinations: Generate Unique Combinations

Files in this package

COMPASS/DESCRIPTION
COMPASS/NAMESPACE
COMPASS/NEWS
COMPASS/R
COMPASS/R/COMPASS-data.R COMPASS/R/COMPASS-discrete.R COMPASS/R/COMPASS-package.R COMPASS/R/COMPASS.R COMPASS/R/COMPASSContainer.R COMPASS/R/COMPASSResult-methods.R COMPASS/R/CellCounts.R COMPASS/R/Combinations.R COMPASS/R/GatingSetToCOMPASS.R COMPASS/R/GetThresholdedIntensities.R COMPASS/R/Posterior.R COMPASS/R/RcppExports.R COMPASS/R/Scores.R COMPASS/R/SimpleCOMPASS.R COMPASS/R/TotalCounts.R COMPASS/R/UniqueCombinations.R COMPASS/R/check_meta.R COMPASS/R/cleanup.R COMPASS/R/commonPlot.R COMPASS/R/description.R COMPASS/R/melt_.R COMPASS/R/merge-COMPASSContainer.R COMPASS/R/miscellaneous.R COMPASS/R/pheatmap.R COMPASS/R/plotMeanGamma-2.R COMPASS/R/plotMeanGamma.R COMPASS/R/shinyCOMPASS.R COMPASS/R/shinyCOMPASSDeps.R COMPASS/R/subset-COMPASSContainer.R COMPASS/R/swap.R COMPASS/R/transpose_list.R COMPASS/R/utils.R COMPASS/R/zzz.R
COMPASS/README.md
COMPASS/build
COMPASS/build/vignette.rds
COMPASS/cleanup
COMPASS/data
COMPASS/data/COMPASS.rda
COMPASS/examples
COMPASS/incubator
COMPASS/inst
COMPASS/inst/doc
COMPASS/inst/doc/COMPASS.R
COMPASS/inst/doc/COMPASS.Rmd
COMPASS/inst/doc/COMPASS.html
COMPASS/inst/shiny
COMPASS/inst/shiny/common_functions.R
COMPASS/inst/shiny/scripts.js
COMPASS/inst/shiny/server.R
COMPASS/inst/shiny/ui.R
COMPASS/inst/shiny/withHelp.R
COMPASS/inst/shiny/www
COMPASS/inst/shiny/www/css
COMPASS/inst/shiny/www/css/shinySplom.css
COMPASS/inst/shiny/www/css/styles.css
COMPASS/inst/shiny/www/jquery-ui
COMPASS/inst/shiny/www/jquery-ui/css
COMPASS/inst/shiny/www/jquery-ui/css/ui-lightness
COMPASS/inst/shiny/www/jquery-ui/css/ui-lightness/images
COMPASS/inst/shiny/www/jquery-ui/css/ui-lightness/images/animated-overlay.gif
COMPASS/inst/shiny/www/jquery-ui/css/ui-lightness/images/ui-bg_diagonals-thick_18_b81900_40x40.png
COMPASS/inst/shiny/www/jquery-ui/css/ui-lightness/images/ui-bg_diagonals-thick_20_666666_40x40.png
COMPASS/inst/shiny/www/jquery-ui/css/ui-lightness/images/ui-bg_flat_10_000000_40x100.png
COMPASS/inst/shiny/www/jquery-ui/css/ui-lightness/images/ui-bg_glass_100_f6f6f6_1x400.png
COMPASS/inst/shiny/www/jquery-ui/css/ui-lightness/images/ui-bg_glass_100_fdf5ce_1x400.png
COMPASS/inst/shiny/www/jquery-ui/css/ui-lightness/images/ui-bg_glass_65_ffffff_1x400.png
COMPASS/inst/shiny/www/jquery-ui/css/ui-lightness/images/ui-bg_gloss-wave_35_f6a828_500x100.png
COMPASS/inst/shiny/www/jquery-ui/css/ui-lightness/images/ui-bg_highlight-soft_100_eeeeee_1x100.png
COMPASS/inst/shiny/www/jquery-ui/css/ui-lightness/images/ui-bg_highlight-soft_75_ffe45c_1x100.png
COMPASS/inst/shiny/www/jquery-ui/css/ui-lightness/images/ui-icons_222222_256x240.png
COMPASS/inst/shiny/www/jquery-ui/css/ui-lightness/images/ui-icons_228ef1_256x240.png
COMPASS/inst/shiny/www/jquery-ui/css/ui-lightness/images/ui-icons_ef8c08_256x240.png
COMPASS/inst/shiny/www/jquery-ui/css/ui-lightness/images/ui-icons_ffd27a_256x240.png
COMPASS/inst/shiny/www/jquery-ui/css/ui-lightness/images/ui-icons_ffffff_256x240.png
COMPASS/inst/shiny/www/jquery-ui/css/ui-lightness/jquery-ui-1.10.3.custom.css
COMPASS/inst/shiny/www/jquery-ui/css/ui-lightness/jquery-ui-1.10.3.custom.min.css
COMPASS/inst/shiny/www/jquery-ui/js
COMPASS/inst/shiny/www/jquery-ui/js/jquery-1.9.1.js
COMPASS/inst/shiny/www/jquery-ui/js/jquery-ui-1.10.3.custom.js
COMPASS/inst/shiny/www/jquery-ui/js/jquery-ui-1.10.3.custom.min.js
COMPASS/inst/shiny/www/js
COMPASS/inst/shiny/www/js/d3.js
COMPASS/inst/shiny/www/js/fancyboxify.js
COMPASS/inst/shiny/www/js/gridsterExtras.js
COMPASS/inst/shiny/www/js/resize.js
COMPASS/inst/shiny/www/js/shinySplom.js
COMPASS/inst/shiny/www/js/tooltips.js
COMPASS/inst/shiny/www/js/updateSubsets.js
COMPASS/inst/shiny/www/multiselect
COMPASS/inst/shiny/www/multiselect/multiselect.css
COMPASS/inst/shiny/www/multiselect/multiselect.js
COMPASS/inst/shiny/www/opentip
COMPASS/inst/shiny/www/opentip/opentip.css
COMPASS/inst/shiny/www/opentip/opentip.js
COMPASS/internal
COMPASS/man
COMPASS/man/COMPASS-package.Rd COMPASS/man/COMPASS.Rd COMPASS/man/COMPASSContainer-data.Rd COMPASS/man/COMPASSContainer.Rd COMPASS/man/COMPASSContainerFromGatingSet.Rd COMPASS/man/COMPASSDescription.Rd COMPASS/man/COMPASSResult-accessors.Rd COMPASS/man/COMPASSResult-data.Rd COMPASS/man/CellCounts.Rd COMPASS/man/Combinations.Rd COMPASS/man/FunctionalityScore.Rd COMPASS/man/GetThresholdedIntensities.Rd COMPASS/man/PolyfunctionalityScore.Rd COMPASS/man/Posterior.Rd COMPASS/man/SimpleCOMPASS.Rd COMPASS/man/TotalCellCounts.Rd COMPASS/man/UniqueCombinations.Rd COMPASS/man/categories.Rd COMPASS/man/markers.Rd COMPASS/man/melt_.Rd COMPASS/man/merge.COMPASSContainer.Rd COMPASS/man/metadata.Rd COMPASS/man/pheatmap.Rd COMPASS/man/plot.COMPASSResult.Rd COMPASS/man/plot2.Rd COMPASS/man/print.COMPASSContainer.Rd COMPASS/man/print.COMPASSResult.Rd COMPASS/man/scores.Rd COMPASS/man/shinyCOMPASS.Rd COMPASS/man/shinyCOMPASSDeps.Rd COMPASS/man/subset.COMPASSContainer.Rd COMPASS/man/summary.COMPASSContainer.Rd COMPASS/man/summary.COMPASSResult.Rd COMPASS/man/transpose_list.Rd
COMPASS/refactor
COMPASS/scratch
COMPASS/src
COMPASS/src/COMPASS_init.c
COMPASS/src/CellCounts.cpp
COMPASS/src/CellCounts_character.cpp
COMPASS/src/Makevars
COMPASS/src/Makevars.win
COMPASS/src/RcppExports.cpp
COMPASS/src/digamma.c
COMPASS/src/mat2vec.c
COMPASS/src/melt_dataframe.c
COMPASS/src/melt_matrix.c
COMPASS/src/samplePuPs.cpp
COMPASS/src/transpose_list.c
COMPASS/src/updatealphas_Exp.cpp
COMPASS/src/updatealphau.cpp
COMPASS/src/updatealphau_noPu_Exp.cpp
COMPASS/src/updatebeta_RW.cpp
COMPASS/src/updategammak_noPu.cpp
COMPASS/src/utils.c
COMPASS/tests
COMPASS/tests/test-all.R
COMPASS/tests/testthat
COMPASS/tests/testthat/helper-init.R
COMPASS/tests/testthat/test-COMPASS.R
COMPASS/tests/testthat/test-CellCounts.R
COMPASS/tests/testthat/test-FunctionalityScore.R
COMPASS/tests/testthat/test-GatingSet2COMPASS.R
COMPASS/vignettes
COMPASS/vignettes/COMPASS.Rmd

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