DOI: 10.18129/B9.bioc.COMPASS  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see COMPASS.

Combinatorial Polyfunctionality Analysis of Single Cells

Bioconductor version: 3.16

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>

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biocViews FlowCytometry, ImmunoOncology, Software
Version 1.36.2
In Bioconductor since BioC 2.14 (R-3.1) (9 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, foreach, coda
LinkingTo Rcpp (>= 0.11.0)
Suggests flowWorkspace(>= 3.33.1), flowCore, ncdfFlow, shiny, testthat, devtools, flowWorkspaceData, ggplot2, progress
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