COMPASS
Combinatorial Polyfunctionality Analysis of Single Cells
Bioconductor version: Release (3.19)
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("COMPASS")
):
Installation
To install this package, start R (version "4.4") 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 | R Script | |
Reference Manual | ||
NEWS | Text |
Details
biocViews | FlowCytometry, ImmunoOncology, Software |
Version | 1.42.0 |
In Bioconductor since | BioC 2.14 (R-3.1) (10.5 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_1.42.0.tar.gz |
Windows Binary | COMPASS_1.42.0.zip |
macOS Binary (x86_64) | COMPASS_1.42.0.tgz |
macOS Binary (arm64) | COMPASS_1.42.0.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 |