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To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("COMPASS")
In most cases, you don't need to download the package archive at all.
COMPASS
Combinatorial Polyfunctionality Analysis of Single Cells
Bioconductor version: 3.0
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 [aut], Kevin Ushey [aut], Greg Finak [aut, cre], Raivo Kolde [ctb] (Author of 'pheatmap', which was modified and now used internally in COMPASS)
Maintainer: Greg Finak <gfinak at fhcrc.org>
Citation (from within R,
enter citation("COMPASS")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("COMPASS")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("COMPASS")
| HTML | R Script | COMPASS |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | FlowCytometry, Software |
| Version | 1.4.0 |
| In Bioconductor since | BioC 2.14 (R-3.1) |
| License | Artistic-2.0 |
| Depends | R (>= 3.0.2) |
| Imports | Rcpp, data.table, RColorBrewer, scales, grid, plyr, knitr, abind, clue, grDevices, utils |
| LinkingTo | Rcpp (>= 0.11.0) |
| Suggests | flowWorkspace(>= 3.9.66), shiny, testthat, devtools, Kmisc |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | COMPASS_1.4.0.tar.gz |
| Windows Binary | COMPASS_1.4.0.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | COMPASS_1.4.0.tgz |
| Mac OS X 10.9 (Mavericks) | COMPASS_1.4.0.tgz |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
- RNA-Seq workflow: gene-level exploratory analysis and differential expression
- Changing genomic coordinate systems with rtracklayer::liftOver
- Mass spectrometry and proteomics data analysis
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