CTDquerier

This package is for version 3.10 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

DOI: 10.18129/B9.bioc.CTDquerier

Bioconductor version: 3.10

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews BiomedicalInformatics, DataImport, DataRepresentation, GO, GeneSetEnrichment, Infrastructure, KEGG, Network, NetworkEnrichment, Pathways, Software

Version 1.5.0

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

URL

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_1.5.0.tar.gz

Windows Binary CTDquerier_1.5.0.zip

Mac OS X 10.11 (El Capitan) CTDquerier_1.5.0.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 3.10 Source Archive