COMPASS: Combinatorial Polyfunctionality Analysis of Single Cells

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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.

Author
Lynn Lin, Kevin Ushey, Greg Finak, Ravio Kolde (pheatmap)
Date of publication
None
Maintainer
Greg Finak <gfinak@fhcrc.org>
License
Artistic-2.0
Version
1.12.0

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