Package: CTDquerier 2.15.0

Xavier Escribà-Montagut

CTDquerier: Package for CTDbase data query, visualization and downstream analysis

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.

Authors:Carles Hernandez-Ferrer [aut], Juan R. Gonzalez [aut], Xavier Escribà-Montagut [cre]

CTDquerier_2.15.0.tar.gz
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CTDquerier_2.15.0.tgz(r-4.4-any)CTDquerier_2.15.0.tgz(r-4.3-any)
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CTDquerier.pdf |CTDquerier.html✨
CTDquerier/json (API)

# Install 'CTDquerier' in R:

install.packages('CTDquerier', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

gala - 'CTDdata' for ilustrative purpouses

On BioConductor:CTDquerier-2.15.0(bioc 3.21)CTDquerier-2.14.0(bioc 3.20)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

software biomedicalinformatics infrastructure dataimport datarepresentation genesetenrichment networkenrichment pathways network go kegg

2.30 score 2 scripts 167 downloads 14 exports 62 dependencies

Last updated 2 months agofrom:b79a567c9a. Checks:OK: 1 WARNING: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Dec 19 2024
R-4.5-win	WARNING	Dec 19 2024
R-4.5-linux	WARNING	Dec 19 2024
R-4.4-win	WARNING	Dec 19 2024
R-4.4-mac	WARNING	Dec 19 2024
R-4.3-win	WARNING	Dec 19 2024
R-4.3-mac	WARNING	Dec 19 2024

Exports:download_ctd_chem download_ctd_dise download_ctd_genes enrich get_table get_terms leaf_plot load_ctd_chem load_ctd_dise load_ctd_gene plot query_ctd_chem query_ctd_dise query_ctd_gene

Dependencies:askpass BiocFileCache BiocGenerics bit bit64 bitops blob cachem cli colorspace cpp11 curl DBI dbplyr dplyr fansi farver fastmap filelock generics ggplot2 glue gridExtra gtable httr igraph isoband jsonlite labeling lattice lifecycle magrittr MASS Matrix memoise mgcv mime munsell nlme openssl pillar pkgconfig plogr purrr R6 RColorBrewer RCurl rlang RSQLite S4Vectors scales stringdist stringi stringr sys tibble tidyr tidyselect utf8 vctrs viridisLite withr

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Class CTDdata	CTDdata CTDdata-class enrich,CTDdata-method get_table,CTDdata-method get_terms,CTDdata-method plot,CTDdata,ANY-method
Package for CTDbase data query, data visualization and data analysis.	CTDquerier
Function to download checmicals available in CTDbase	download_ctd_chem
Function to download diseases available in CTDbase	download_ctd_dise
Function to download genes available in CTDbase	download_ctd_genes
Method to perform enrichment analysis using two 'CTDdata' objects	enrich
'CTDdata' for ilustrative purpouses	gala
Method to obtain a specific inner table from a 'CTDdata' object.	get_table
Getter to obtain the terms used to perform a query into CTDbase	get_terms
Function to create a leaf plot	leaf_plot
Function to load the '.tsv.gz' file for chemicals	load_ctd_chem
Function to load the '.tsv.gz' file for disease	load_ctd_dise
Function to load the '.tsv.gz' file for genes	load_ctd_gene
Function to query CTDbase using chemical terminology ( Chemical Name )	query_ctd_chem
Function to query CTDbase using disease terminology	query_ctd_dise
Function to query CTDbase using gene terminology ( Gene Symbol )	query_ctd_gene