hipathia

DOI: 10.18129/B9.bioc.hipathia    

HiPathia: High-throughput Pathway Analysis

Bioconductor version: Release (3.7)

Hipathia is a method for the computation of signal transduction along signaling pathways from transcriptomic data. The method is based on an iterative algorithm which is able to compute the signal intensity passing through the nodes of a network by taking into account the level of expression of each gene and the intensity of the signal arriving to it. It also provides a new approach to functional analysis allowing to compute the signal arriving to the functions annotated to each pathway.

Author: Marta R. Hidalgo [aut, cre], José Carbonell-Caballero [ctb], Francisco Salavert [ctb], Alicia Amadoz [ctb], Çankut Cubuk [ctb], Joaquin Dopazo [ctb]

Maintainer: Marta R. Hidalgo <marta.hidalgo at outlook.es>

Citation (from within R, enter citation("hipathia")):

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("hipathia")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("hipathia")

 

PDF R Script Hipathia Package
PDF   Reference Manual
Text   NEWS

Details

biocViews GO, GeneExpression, GeneSignaling, GraphAndNetwork, Pathways, Software
Version 1.0.0
License GPL-2
Depends R (>= 3.5), igraph (>= 1.0.1), AnnotationHub(>= 2.6.5), MultiAssayExperiment(>= 1.4.9), SummarizedExperiment(>= 1.8.1)
Imports coin, stats, limma, grDevices, utils, graphics, preprocessCore, servr, DelayedArray, matrixStats, methods, S4Vectors
LinkingTo
Suggests BiocStyle, knitr, rmarkdown, testthat
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.

Source Package hipathia_1.0.0.tar.gz
Windows Binary hipathia_1.0.0.zip
Mac OS X 10.11 (El Capitan) hipathia_1.0.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/hipathia
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/hipathia
Package Short Url http://bioconductor.org/packages/hipathia/
Package Downloads Report Download Stats

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