hipathia
HiPathia: High-throughput Pathway Analysis
Bioconductor version: 3.24 · Package version: 3.13.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("hipathia")Details
| Maintainer | Marta R. Hidalgo <marta.hidalgo@outlook.es> |
| Author | Marta R. Hidalgo [aut, cre], José Carbonell-Caballero [ctb], Francisco Salavert [ctb], Alicia Amadoz [ctb], Çankut Cubuk [ctb], Joaquin Dopazo [ctb] |
| License | GPL-2 |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | GO, GeneExpression, GeneSignaling, GraphAndNetwork, Pathways, Software |
| Package Short Url | https://bioconductor.org/packages/hipathia/ |
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 3.13.0, https://bioconductor.org/packages/hipathia.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | hipathia_3.13.0.tar.gz |
| Windows binary (x86_64) | hipathia_3.13.0.zip |
| macOS binary (arm64) | hipathia_3.13.0.tgz |
| macOS binary (x86_64) | hipathia_3.13.0.tgz |
Dependencies
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