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>
citation("COMPASS")):
Installation
To install this package, start R (version "4.0") 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 | 1.28.0 |
| 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, doMC, 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_1.28.0.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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/COMPASS/ |
| Package Short Url | https://bioconductor.org/packages/COMPASS/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.12 | Source Archive |