COMPASS

DOI: 10.18129/B9.bioc.COMPASS    

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see COMPASS.

Combinatorial Polyfunctionality Analysis of Single Cells

Bioconductor version: 3.12

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>

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("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")

 

HTML	R Script	COMPASS
PDF	R Script	SimpleCOMPASS
PDF		Reference Manual
Text		NEWS

Details

biocViews	FlowCytometry, ImmunoOncology, Software
Version	1.28.0
In Bioconductor since	BioC 2.14 (R-3.1) (7 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, doMC, progress
SystemRequirements
Enhances
URL
BugReports	https://github.com/RGLab/COMPASS/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	COMPASS_1.28.0.tar.gz
Windows Binary	COMPASS_1.27.0.zip (32- & 64-bit)
macOS 10.13 (High Sierra)	COMPASS_1.28.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/COMPASS
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/COMPASS
Package Short Url	https://bioconductor.org/packages/COMPASS/
Package Downloads Report	Download Stats