CTDquerier

This package is for version 3.9 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see CTDquerier.

Package for CTDbase data query, visualization and downstream analysis


Bioconductor version: 3.9

Package to retrieve and visualize data from the Comparative Toxicogenomics Database (http://ctdbase.org/). The downloaded data is formated as DataFrames for further downstream analyses.

Author: Carles Hernandez-Ferrer [aut, cre], Jaun R. Gonzalez [aut]

Maintainer: Carles Hernandez-Ferrer <carles.hernandez at isglobal.org>

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

Installation

To install this package, start R (version "3.6") and enter:


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

BiocManager::install("CTDquerier")

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("CTDquerier")
Case study on Environmental Chemicals and asthma-related genes HTML R Script
CTDquerier: A package to retrieve CTDbase data for downstream analysis and data visualization HTML R Script
Simple comparison between CTDquerier R package and CTDbase Batch Query web tool HTML R Script
Reference Manual PDF
LICENSE Text

Details

biocViews BiomedicalInformatics, DataImport, DataRepresentation, GO, GeneSetEnrichment, Infrastructure, KEGG, Network, NetworkEnrichment, Pathways, Software
Version 1.4.0
In Bioconductor since BioC 3.7 (R-3.5) (6 years)
License MIT + file LICENSE
Depends R (>= 3.4.0)
Imports RCurl, stringr, S4Vectors, stringdist, ggplot2, igraph, utils, grid, gridExtra, methods, stats, BiocFileCache, rappdirs
System Requirements
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Suggests BiocStyle, knitr
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Build Report Build Report

Package Archives

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

Source Package CTDquerier_1.4.0.tar.gz
Windows Binary CTDquerier_1.4.0.zip
Mac OS X 10.11 (El Capitan) CTDquerier_1.4.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/CTDquerier
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/CTDquerier
Bioc Package Browser https://code.bioconductor.org/browse/CTDquerier/
Package Short Url https://bioconductor.org/packages/CTDquerier/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.9 Source Archive