Package: customCMPdb 1.23.0

Yuzhu Duan

customCMPdb: Customize and Query Compound Annotation Database

This package serves as a query interface for important community collections of small molecules, while also allowing users to include custom compound collections.

Authors:Yuzhu Duan [aut, cre], Thomas Girke [aut]

customCMPdb_1.23.0.tar.gz
customCMPdb_1.23.0.zip(r-4.7)customCMPdb_1.23.0.zip(r-4.6)customCMPdb_1.23.0.zip(r-4.5)
customCMPdb_1.23.0.tgz(r-4.6-any)customCMPdb_1.23.0.tgz(r-4.5-any)
customCMPdb_1.23.0.tar.gz(r-4.7-any)customCMPdb_1.23.0.tar.gz(r-4.6-any)
customCMPdb_1.23.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
customCMPdb/json (API)
NEWS

# Install 'customCMPdb' in R:

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

Bug tracker:https://github.com/yduan004/customcmpdb/issues

On BioConductor:customCMPdb-1.23.0(bioc 3.24)customCMPdb-1.22.0(bioc 3.23)

software cheminformatics annotationhubsoftware

4.48 score 1 stars 5 scripts 332 downloads 11 exports 95 dependencies

Last updated from:055aeb101d. Checks:1 WARNING, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	169
linux-devel-x86_64	OK	305
source / vignettes	OK	285
linux-release-x86_64	OK	289
macos-release-arm64	OK	211
macos-oldrel-arm64	OK	176
windows-devel	OK	538
windows-release	OK	914
windows-oldrel	OK	203
wasm-release	OK	155

Exports:addCustomAnnot buildDrugAgeDB dbxml2df defaultAnnot deleteAnnot df2SQLite listAnnot loadAnnot loadSDFwithName processDrugage queryAnnotDB

Dependencies:AnnotationDbi AnnotationHub askpass base64enc BH Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocManager BiocVersion Biostrings bit bit64 bitops blob bslib cachem ChemmineR cli cpp11 crayon crosstalk curl DBI dbplyr digest dplyr DT evaluate farver fastmap filelock fontawesome fs generics ggplot2 glue gridExtra gtable highr htmltools htmlwidgets httr httr2 IRanges isoband jquerylib jsonlite KEGGREST knitr labeling later lazyeval lifecycle magrittr memoise mime openssl otel pillar pkgconfig png promises purrr R6 rappdirs RColorBrewer Rcpp RCurl rjson rlang rmarkdown RSQLite rsvg S4Vectors S7 sass scales Seqinfo stringi stringr sys tibble tidyr tidyselect tinytex utf8 vctrs viridisLite withr xfun XML XVector yaml

customCMPdb: Integrating Community and Custom Compound Collections

Authors: Yuzhu Duan, Dan Evans, Kevin Horan, Austin Leong, Siddharth Sai and Thomas Girke

Rendered fromcustomCMPdb.Rmdusingknitr::rmarkdownon May 28 2026.

Last update: 2022-02-01
Started: 2020-10-01

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Customize and Query Compound Annotation Database	customCMPdb-package customCMPdb
Add/Delete Custom Annotation	addCustomAnnot customAnnot defaultAnnot deleteAnnot listAnnot
Build CMAP Database	buildCMAPdb
Build DrugAge Annotation Database	buildDrugAgeDB
Convert drugbank database (xml file) into dataframe.	dbxml2df
Store drugbank dataframe into an SQLite database	df2SQLite
Load Compound Annotation Database	loadAnnot
Load Compound Structures from Four Resources	loadSDFwithName
Process Source DrugAge Dataset	processDrugage
Annotation Queries with Compound IDs	queryAnnotDB