Package: customCMPdb 1.17.0

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_1.17.0.tar.gz
customCMPdb_1.17.0.zip(r-4.5)customCMPdb_1.17.0.zip(r-4.4)customCMPdb_1.17.0.zip(r-4.3)
customCMPdb_1.17.0.tgz(r-4.4-any)customCMPdb_1.17.0.tgz(r-4.3-any)
customCMPdb_1.17.0.tar.gz(r-4.5-noble)customCMPdb_1.17.0.tar.gz(r-4.4-noble)
customCMPdb_1.17.0.tgz(r-4.4-emscripten)customCMPdb_1.17.0.tgz(r-4.3-emscripten)
customCMPdb.pdf |customCMPdb.html✨
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-1.17.0(bioc 3.21)customCMPdb-1.16.0(bioc 3.20)

software cheminformatics annotationhubsoftware

4.78 score 2 stars 4 scripts 184 downloads 11 exports 104 dependencies

Last updated 2 months agofrom:c0072d48e6. Checks:OK: 7. Indexed: yes.

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

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

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

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 Dec 19 2024.

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