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SBGNview.data

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

Supporting datasets for SBGNview package


Bioconductor version: Development (3.19)

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>

Citation (from within R, enter citation("SBGNview.data")):

Installation

To install this package, start R (version "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")
Supporting Datasets for SBGNview Package HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews BreastCancerData, CancerData, ExperimentData, GEO, MicroarrayData, RNASeqData
Version 1.17.0
License AGPL-3
Depends R (>= 3.6)
Imports knitr, rmarkdown, bookdown
System Requirements
URL
See More
Suggests SummarizedExperiment
Linking To
Enhances
Depends On Me SBGNview
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 SBGNview.data_1.17.0.tar.gz
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
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/
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