hipathia

DOI: 10.18129/B9.bioc.hipathia    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see hipathia.

HiPathia: High-throughput Pathway Analysis

Bioconductor version: 3.9

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>

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("hipathia")

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("hipathia")

 

PDF	R Script	Hipathia Package
PDF		Reference Manual
Text		NEWS

Details

biocViews	GO, GeneExpression, GeneSignaling, GraphAndNetwork, Pathways, Software
Version	2.0.0
In Bioconductor since	BioC 3.7 (R-3.5) (1.5 years)
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
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	hipathia_2.0.0.tar.gz
Windows Binary	hipathia_2.0.0.zip
Mac OS X 10.11 (El Capitan)	hipathia_2.0.0.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	https://bioconductor.org/packages/hipathia/
Package Downloads Report	Download Stats