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>

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

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

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: