To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("ASSIGN")
In most cases, you don't need to download the package archive at all.
ASSIGN
Adaptive Signature Selection and InteGratioN (ASSIGN)
Bioconductor version: 2.14
ASSIGN is a computational tool to evaluate the pathway deregulation/activation status in individual patient samples. ASSIGN employs a flexible Bayesian factor analysis approach that adapts predetermined pathway signatures derived either from knowledge-based literatures or from perturbation experiments to the cell-/tissue-specific pathway signatures. The deregulation/activation level of each context-specific pathway is quantified to a score, which represents the extent to which a patient sample encompasses the pathway deregulation/activation signature.
Author: Ying Shen, Andrea H. Bild, and W. Evan Johnson
Maintainer: Ying Shen <yshen3 at bu.edu>
Citation (from within R,
enter citation("ASSIGN")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("ASSIGN")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("ASSIGN")
| R Script | Primer | |
| Reference Manual |
Details
| biocViews | Bayesian, GeneExpression, Pathways, Software |
| Version | 1.0.0 |
| In Bioconductor since | BioC 2.14 (R-3.1) |
| License | MIT |
| Depends | Rlab, msm, gplots |
| Imports | graphics, grDevices, stats, utils |
| Suggests | |
| System Requirements | |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | ASSIGN_1.0.0.tar.gz |
| Windows Binary | ASSIGN_1.0.0.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | ASSIGN_1.0.0.tgz |
| Mac OS X 10.9 (Mavericks) | ASSIGN_1.0.0.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
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