hipathia

This is the released version of hipathia; for the devel version, see hipathia.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7

HiPathia: High-throughput Pathway Analysis

Bioconductor version: Release (3.23)

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")):

Marta R. Hidalgo. hipathia: HiPathia: High-throughput Pathway Analysis. doi:10.18129/B9.bioc.hipathia, R package version 3.12.0, https://bioconductor.org/packages/hipathia.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

if (!require("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")

Hipathia Package	PDF	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	GO, GeneExpression, GeneSignaling, GraphAndNetwork, Pathways, Software
Version	3.12.0
In Bioconductor since	BioC 3.7 (R-3.5) (8.5 years)
License	GPL-2
Depends	R (>= 4.1), igraph (>= 1.0.1), zen4R (>= 0.10.4), 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
System Requirements
URL

Suggests	BiocStyle, knitr, rmarkdown, testthat
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	hipathia_3.12.0.tar.gz
Windows Binary (x86_64)	hipathia_3.12.0.zip (64-bit only)
macOS Binary (big-sur-x86_64)	hipathia_3.12.0.tgz
macOS Binary (sonoma-arm64)	hipathia_3.12.0.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