pathifier
This is the development version of pathifier; for the stable release version, see pathifier.
Quantify deregulation of pathways in cancer
Bioconductor version: Development (3.24)
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("pathifier")):
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")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("pathifier")
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("pathifier")| Quantify deregulation of pathways in cancer | R Script | |
| Reference Manual |
Details
| biocViews | Network, Software |
| Version | 1.51.0 |
| In Bioconductor since | BioC 2.13 (R-3.0) (13 years) |
| License | Artistic-1.0 |
| Depends | |
| Imports | R.oo, princurve (>= 2.0.4) |
| System Requirements | |
| URL |
See More
| Suggests | |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | funOmics |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | pathifier_1.51.0.tar.gz |
| Windows Binary (x86_64) | pathifier_1.51.0.zip |
| macOS Binary (big-sur-x86_64) | pathifier_1.51.0.tgz |
| macOS Binary (sonoma-arm64) | pathifier_1.51.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/pathifier |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/pathifier |
| Bioc Package Browser | https://code.bioconductor.org/browse/pathifier/ |
| Package Short Url | https://bioconductor.org/packages/pathifier/ |
| Package Downloads Report | Download Stats |