COMPASS
This is the released version of COMPASS; for the devel version, see COMPASS.
Combinatorial Polyfunctionality Analysis of Single Cells
Bioconductor version: Release (3.23)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | 1.49.0 |
| In Bioconductor since | BioC 2.14 (R-3.1) (12.5 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_1.49.0.tar.gz |
| Windows Binary (x86_64) | COMPASS_1.49.0.zip |
| macOS Binary (big-sur-x86_64) | COMPASS_1.49.0.tgz |
| macOS Binary (sonoma-arm64) | COMPASS_1.49.0.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 |