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COMPASS

Combinatorial Polyfunctionality Analysis of Single Cells


Bioconductor version: Release (3.18)

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 fhcrc.org>

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

Installation

To install this package, start R (version "4.3") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("COMPASS")

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

Documentation

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

browseVignettes("COMPASS")
COMPASS HTML R Script
SimpleCOMPASS PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews FlowCytometry, ImmunoOncology, Software
Version 1.40.0
In Bioconductor since BioC 2.14 (R-3.1) (10 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
System Requirements
URL
Bug Reports https://github.com/RGLab/COMPASS/issues
See More
Suggests flowWorkspace(>= 3.33.1), flowCore, ncdfFlow, shiny, testthat, devtools, flowWorkspaceData, ggplot2, progress
Linking To Rcpp (>= 0.11.0)
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package COMPASS_1.40.0.tar.gz
Windows Binary COMPASS_1.40.0.zip
macOS Binary (x86_64) COMPASS_1.40.0.tgz
macOS Binary (arm64) COMPASS_1.40.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/COMPASS
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/COMPASS
Bioc Package Browser https://code.bioconductor.org/browse/COMPASS/
Package Short Url https://bioconductor.org/packages/COMPASS/
Package Downloads Report Download Stats