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To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("pathifier")
In most cases, you don't need to download the package archive at all.
pathifier
Quantify deregulation of pathways in cancer
Bioconductor version: 2.14
Pathifier is an algorithm that infers pathway deregulation scores for each tumor sample on the basis of expression data. This score is determined, in a context-specific manner, for every particular dataset and type of cancer that is being investigated. The algorithm transforms gene-level information into pathway-level information, generating a compact and biologically relevant representation of each sample.
Author: Yotam Drier
Maintainer: Assif Yitzhaky <assif.yitzhaky at weizmann.ac.il>
Citation (from within R,
enter citation("pathifier")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("pathifier")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("pathifier")
| R Script | Quantify deregulation of pathways in cancer | |
| Reference Manual |
Details
| biocViews | Network, Software |
| Version | 1.2.0 |
| In Bioconductor since | BioC 2.13 (R-3.0) |
| License | Artistic-1.0 |
| Depends | |
| Imports | R.oo, princurve |
| 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 | pathifier_1.2.0.tar.gz |
| Windows Binary | pathifier_1.2.0.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | pathifier_1.2.0.tgz |
| Mac OS X 10.9 (Mavericks) | pathifier_1.2.0.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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