Package: biodbNcbi 1.11.0

Pierrick Roger

biodbNcbi: biodbNcbi, a library for connecting to NCBI Databases.

The biodbNcbi library provides access to the NCBI databases CCDS, Gene, Pubchem Comp and Pubchem Subst, using biodb package framework. It allows to retrieve entries by their accession number. Web services can be accessed for searching the database by name or mass.

Authors:Pierrick Roger [aut, cre]

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biodbNcbi.pdf |biodbNcbi.html✨
biodbNcbi/json (API)
NEWS

# Install 'biodbNcbi' in R:

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

Bug tracker:https://github.com/pkrog/biodbncbi/issues

On BioConductor:biodbNcbi-1.11.0(bioc 3.21)biodbNcbi-1.10.0(bioc 3.20)

software infrastructure dataimport

4.00 score 1 stars 1 scripts 190 downloads 11 exports 70 dependencies

Last updated 5 months agofrom:4a3f8f2cfd. Checks:1 OK, 8 NOTE. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Mar 19 2025
R-4.5-win	NOTE	Mar 19 2025
R-4.5-mac	NOTE	Mar 19 2025
R-4.5-linux	NOTE	Mar 19 2025
R-4.4-win	NOTE	Mar 19 2025
R-4.4-mac	NOTE	Mar 19 2025
R-4.4-linux	NOTE	Mar 19 2025
R-4.3-win	NOTE	Mar 19 2025
R-4.3-mac	NOTE	Mar 19 2025

Exports:NcbiCcdsConn NcbiCcdsEntry NcbiEntrezConn NcbiGeneConn NcbiGeneEntry NcbiPubchemCompConn NcbiPubchemCompEntry NcbiPubchemConn NcbiPubchemEntry NcbiPubchemSubstConn NcbiPubchemSubstEntry

Dependencies:askpass BiocFileCache biodb bit bit64 bitops blob brio cachem callr chk cli cpp11 crayon curl DBI dbplyr desc diffobj digest dplyr evaluate fansi fastmap filelock fs generics git2r glue hms httr jsonlite lgr lifecycle magrittr memoise mime openssl pillar pkgbuild pkgconfig pkgload plogr plyr praise prettyunits processx progress ps purrr R6 rappdirs Rcpp RCurl rlang rprojroot RSQLite stringi stringr sys testthat tibble tidyr tidyselect utf8 vctrs waldo withr XML yaml

An introduction to biodbNcbi

Pierrick Roger

Rendered frombiodbNcbi.Rmdusingknitr::rmarkdownon Mar 19 2025.

Last update: 2022-03-24
Started: 2022-03-03

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
biodbNcbi: biodbNcbi, a library for connecting to NCBI Databases.	biodbNcbi-package biodbNcbi
NCBI CCDS connector class.	NcbiCcdsConn
NCBI CCDS entry class.	NcbiCcdsEntry
NCBI Entrez connector abstract class.	NcbiEntrezConn
NCBI Gene connector class.	NcbiGeneConn
NCBI Gene entry class.	NcbiGeneEntry
NCBI PubChem Compound connector class.	NcbiPubchemCompConn
NCBI PubChem Compound entry class.	NcbiPubchemCompEntry
NCBI PubChem connector abstractclass.	NcbiPubchemConn
NCBI PubChem entry class.	NcbiPubchemEntry
NCBI PubChem Substance connector class.	NcbiPubchemSubstConn
NCBI PubChem Substance entry class.	NcbiPubchemSubstEntry