SBGNview.data

DOI: 10.18129/B9.bioc.SBGNview.data    

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see SBGNview.data.

Demo gene expression datasets for SBGNview package

Bioconductor version: 3.12

This package contains: 1. A microarray gene expression dataset from a human breast cancer study. 2. A RNA-Seq gene expression dataset from a mouse study on IFNG knockout. 3. ID mapping tables between gene IDs and SBGN-ML file glyph IDs. 4. Percent of orthologs detected in other species of the genes in a pathway. Cutoffs of this percentage for defining if a pathway exists in another species. 5. XML text of SBGN-ML files for all pre-collected pathways.

Author: Xiaoxi Dong*, Kovidh Vegesna*, Weijun Luo

Maintainer: Weijun Luo <luo_weijun at yahoo.com>

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("SBGNview.data")

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("SBGNview.data")

 

HTML	R Script	SBGNview functions
PDF		Reference Manual
Text		NEWS

Details

biocViews	BreastCancerData, CancerData, ExperimentData, GEO, MicroarrayData, RNASeqData
Version	1.4.1
License	AGPL-3
Depends	R (>= 3.6)
Imports	knitr, rmarkdown, bookdown
LinkingTo
Suggests	SummarizedExperiment
SystemRequirements
Enhances
URL
Depends On Me	SBGNview
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	SBGNview.data_1.4.1.tar.gz
Windows Binary
macOS 10.13 (High Sierra)
Source Repository	git clone https://git.bioconductor.org/packages/SBGNview.data
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/SBGNview.data
Package Short Url	https://bioconductor.org/packages/SBGNview.data/
Package Downloads Report	Download Stats