punKEGGer
This is the development version of punKEGGer; to use it, please install the devel version of Bioconductor.
Parse, Expand, Annotate and Visualize KEGG Pathway Networks as Tidy Graphs
Bioconductor version: Development (3.24)
Provides tools to parse KEGG pathway KGML files into tidy graphs, expand metanodes (e.g., multi-gene entries), annotate them with custom dictionaries, and produce consistent visualizations using ggraph. Enables integration of KEGG pathways with tidygraph-based workflows.
Author: Guillermo de Anda Jáuregui [aut, cre]
Maintainer: Guillermo de Anda Jáuregui <gdeanda at inmegen.edu.mx>
citation("punKEGGer")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("punKEGGer")
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("punKEGGer")| punKEGGer: parsing and visualization of KEGG pathways for network science | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | GraphAndNetwork, KEGG, Network, Pathways, Software, Visualization |
| Version | 0.99.65 |
| In Bioconductor since | BioC 3.24 (R-4.6) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.6.0) |
| Imports | dplyr, ggplot2, ggraph, glue, igraph, purrr, rlang, stringr, tibble, tidygraph, tidyselect, tidyr, KEGGREST, xml2 |
| System Requirements | |
| URL | https://github.com/guillermodeandajauregui/punKEGGer |
| Bug Reports | https://github.com/guillermodeandajauregui/punKEGGer/issues |
See More
| Suggests | testthat (>= 3.0.0), knitr, rmarkdown, BiocStyle, XML |
| 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 | punKEGGer_0.99.65.tar.gz |
| Windows Binary (x86_64) | punKEGGer_0.99.65.zip |
| macOS Binary (big-sur-x86_64) | punKEGGer_0.99.65.tgz |
| macOS Binary (sonoma-arm64) | punKEGGer_0.99.65.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/punKEGGer |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/punKEGGer |
| Bioc Package Browser | https://code.bioconductor.org/browse/punKEGGer/ |
| Package Short Url | https://bioconductor.org/packages/punKEGGer/ |
| Package Downloads Report | Download Stats |