hipathia
This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see hipathia.
HiPathia: High-throughput Pathway Analysis
Bioconductor version: 3.17
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("hipathia")):
Installation
To install this package, start R (version "4.3") 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 | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | GO, GeneExpression, GeneSignaling, GraphAndNetwork, Pathways, Software |
| Version | 3.0.2 |
| 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 |
| System Requirements | |
| URL |
See More
| Suggests | BiocStyle, knitr, rmarkdown, testthat |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | hipathia_3.0.2.tar.gz |
| Windows Binary | hipathia_3.0.2.zip (64-bit only) |
| macOS Binary (x86_64) | hipathia_3.0.2.tgz |
| macOS Binary (arm64) | hipathia_3.0.2.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 |
| Old Source Packages for BioC 3.17 | Source Archive |