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

Functions

categories Man page
CC Man page
CellCounts Man page
Combinations Man page
COMPASS Man page
COMPASSContainer Man page
COMPASSContainer-data Man page
COMPASSContainerFromGatingSet Man page
COMPASSDescription Man page
COMPASSDescription<- Man page
COMPASS-package Man page
COMPASSResult-accessors Man page
COMPASSResult-data Man page
CR Man page
FunctionalityScore Man page
FunctionalityScore.COMPASSResult Man page
FunctionalityScore.default Man page
Gamma Man page
GetThresholdedIntensities Man page
markers Man page
MeanGamma Man page
melt_ Man page
melt_.data.frame Man page
melt_.matrix Man page
merge.COMPASSContainer Man page
metadata Man page
metadata<- Man page
metadata<-.COMPASSContainer Man page
metadata.COMPASSContainer Man page
metadata.COMPASSResult Man page
pheatmap Man page
plot Man page
plot2 Man page
plot.COMPASSResult Man page
PolyfunctionalityScore Man page
PolyfunctionalityScore.COMPASSResult Man page
PolyfunctionalityScore.default Man page
Posterior Man page
PosteriorDiff Man page
PosteriorLogDiff Man page
PosteriorPs Man page
PosteriorPu Man page
print.COMPASSContainer Man page
print.COMPASSResult Man page
scores Man page
shinyCOMPASS Man page
shinyCOMPASSDeps Man page
SimpleCOMPASS Man page
subset.COMPASSContainer Man page
summary.COMPASSContainer Man page
summary.COMPASSResult Man page
TotalCellCounts Man page
transpose_list Man page
UniqueCombinations Man page
UniqueCombinations.COMPASSContainer Man page
UniqueCombinations.default Man page

Files

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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