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hipathia

This is the development version of hipathia; for the stable release version, see hipathia.

HiPathia: High-throughput Pathway Analysis


Bioconductor version: Development (3.19)

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 (version "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")
Hipathia Package PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews GO, GeneExpression, GeneSignaling, GraphAndNetwork, Pathways, Software
Version 3.3.0
In Bioconductor since BioC 3.7 (R-3.5) (6 years)
License GPL-2
Depends R (>= 4.1), 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, ggplot2, ggpubr, dplyr, tibble, visNetwork, reshape2, MetBrewer
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Suggests BiocStyle, knitr, rmarkdown, testthat
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Package Archives

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

Source Package hipathia_3.3.0.tar.gz
Windows Binary hipathia_3.3.0.zip
macOS Binary (x86_64) hipathia_3.3.0.tgz
macOS Binary (arm64) hipathia_3.3.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/hipathia
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/hipathia
Bioc Package Browser https://code.bioconductor.org/browse/hipathia/
Package Short Url https://bioconductor.org/packages/hipathia/
Package Downloads Report Download Stats