pathRender

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This is the development version of pathRender; for the stable release version, see pathRender.

Render molecular pathways

Bioconductor version: Development (3.24)

build graphs from pathway databases, render them by Rgraphviz.

Author: Li Long <lilong at isb-sib.ch>

Maintainer: Vince Carey <stvjc at channing.harvard.edu>

Citation (from within R, enter citation("pathRender")):

Seminal Bioconductor project articles:

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("pathRender")

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("pathRender")

pathRender overview	PDF	R Script
pathway graphs colored by expression map	PDF	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	GraphAndNetwork, Pathways, Software, Visualization
Version	1.81.1
In Bioconductor since	BioC 1.8 (R-2.3) (20.5 years)
License	LGPL
Depends	graph, Rgraphviz, RColorBrewer, cMAP, AnnotationDbi, methods, stats4
Imports
System Requirements
URL	http://www.bioconductor.org

Suggests	ALL, hgu95av2.db
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	pathRender_1.81.1.tar.gz
Windows Binary (x86_64)
macOS Binary (big-sur-x86_64)	pathRender_1.81.1.tgz
macOS Binary (sonoma-arm64)	pathRender_1.81.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/pathRender
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/pathRender
Package Short Url	https://bioconductor.org/packages/pathRender/
Package Downloads Report	Download Stats