COMPASS

DOI: 10.18129/B9.bioc.COMPASS    

Combinatorial Polyfunctionality Analysis of Single Cells

Bioconductor version: Release (3.6)

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 and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("COMPASS")

Documentation

HTML	R Script	COMPASS
PDF		Reference Manual
Text		NEWS

Details

biocViews	FlowCytometry, Software
Version	1.16.2
In Bioconductor since	BioC 2.14 (R-3.1) (4 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
LinkingTo	Rcpp (>= 0.11.0)
Suggests	flowWorkspace(>= 3.9.66), flowCore, ncdfFlow, shiny, testthat, devtools, flowWorkspaceData
SystemRequirements
Enhances
URL
BugReports	https://github.com/RGLab/COMPASS/issues
Depends On Me
Imports Me
Suggests Me
Build Report

Package Archives

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

Source Package	COMPASS_1.16.2.tar.gz
Windows Binary	COMPASS_1.16.2.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	COMPASS_1.16.2.tgz
Source Repository	git clone https://git.bioconductor.org/packages/COMPASS
Package Short Url	http://bioconductor.org/packages/COMPASS/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.6	Source Archive