PinPath
This is the development version of PinPath; to use it, please install the devel version of Bioconductor.
Visualization of Omics Data onto Pathway Diagrams
Bioconductor version: Development (3.24)
PinPath enables flexible visualization of (omics) data onto pathways diagrams, allowing users to pinpoint where the relevant changes occur. It supports pathway diagrams from WikiPathways and KEGG, as well as custom GPML and KGML files. Data can be displayed on both native pathway layouts and network representations.
Author: Jarno Koetsier [aut, cre]
, Lars Eijssen [aut]
, Egon Willighagen [aut]
, Stichting Terre - The Dutch Rett Syndrome Foundation [fnd]
Maintainer: Jarno Koetsier <jarno.koetsier at gmail.com>
citation("PinPath")):
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("PinPath")
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("PinPath")| 1. WikiPathways visualization | HTML | R Script |
| 2. KEGG visualization | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | GraphAndNetwork, KEGG, Metabolomics, Network, Pathways, Proteomics, Software, Transcriptomics, Visualization |
| Version | 0.99.4 |
| In Bioconductor since | BioC 3.24 (R-4.6) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.6.0) |
| Imports | grDevices, graphics, stats, XML, xml2, magrittr, dplyr, tidyr, stringr, magick, shape, grid, gridBase, svglite, AnnotationDbi, igraph, ggraph, ggplot2, BiocFileCache, BiocGenerics, rlang |
| System Requirements | |
| URL | https://github.com/SyNUM-lab/PinPath |
| Bug Reports | https://github.com/SyNUM-lab/PinPath/issues |
See More
| Suggests | testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown, rWikiPathways, org.Hs.eg.db, metaboliteIDmapping |
| 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 | PinPath_0.99.4.tar.gz |
| Windows Binary (x86_64) | PinPath_0.99.4.zip |
| macOS Binary (big-sur-x86_64) | PinPath_0.99.4.tgz |
| macOS Binary (sonoma-arm64) | PinPath_0.99.4.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/PinPath |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/PinPath |
| Bioc Package Browser | https://code.bioconductor.org/browse/PinPath/ |
| Package Short Url | https://bioconductor.org/packages/PinPath/ |
| Package Downloads Report | Download Stats |