DOI: 10.18129/B9.bioc.COMPASS    

Combinatorial Polyfunctionality Analysis of Single Cells

Bioconductor version: Release (3.8)

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)

Maintainer: Greg Finak <gfinak at>

Citation (from within R, enter citation("COMPASS")):


To install this package, start R (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
BiocManager::install("COMPASS", version = "3.8")

For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:



PDF R Script SimpleCOMPASS
PDF   Reference Manual
Text   NEWS


biocViews FlowCytometry, ImmunoOncology, Software
Version 1.20.1
In Bioconductor since BioC 2.14 (R-3.1) (5 years)
License Artistic-2.0
Depends R (>= 3.0.3)
Imports methods, Rcpp, data.table, RColorBrewer, scales, grid, plyr, knitr, abind, clue, grDevices, utils, pdist, magrittr, reshape2, dplyr, tidyr, rlang, BiocStyle, rmarkdown
LinkingTo Rcpp (>= 0.11.0)
Suggests flowWorkspace(>= 3.9.66), flowCore, ncdfFlow, shiny, testthat, devtools, flowWorkspaceData
Depends On Me
Imports Me
Suggests Me
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Follow Installation instructions to use this package in your R session.

Source Package COMPASS_1.20.1.tar.gz
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Mac OS X 10.11 (El Capitan) COMPASS_1.20.1.tgz
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