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
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("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 | ||
| LICENSE | Text |
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 |
See More
| Suggests | BiocStyle, knitr |
| 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 | 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 |