Introduction | Installation and Loading | Overview | DrugAge Annotations | DrugAge SDF | DrugBank SDF | CMAP SDF | LINCS SDF | Custom Annotation Database | Load Annotation Database | Add Custom Annotation Tables | Delete Custom Annotation Tables | Set to Default | Query Annotation Database | Supplemental Material | Description of Annotation Tables in SQLite Database | Session Info | References
Package: customCMPdb 1.22.0
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:
customCMPdb_1.22.0.tar.gz
customCMPdb_1.22.0.zip(r-4.7-any)customCMPdb_1.22.0.zip(r-4.6-any)customCMPdb_1.22.0.zip(r-4.5-any)
customCMPdb_1.22.0.tgz(r-4.6-any)customCMPdb_1.22.0.tgz(r-4.5-any)
customCMPdb_1.22.0.tar.gz(r-4.7-any)customCMPdb_1.22.0.tar.gz(r-4.6-any)
customCMPdb_1.22.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
customCMPdb/json (API)
| # Install 'customCMPdb' in R: |
| install.packages('customCMPdb', repos = c('https://bioc-release.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)
softwarecheminformaticsannotationhubsoftware
Last updated from:9c12128f61 (on RELEASE_3_23). Checks:1 WARNING, 9 OK. Indexed: no.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 138 | ||
| linux-devel | OK | 292 | ||
| source / vignettes | OK | 346 | ||
| linux-release | OK | 284 | ||
| macos-release | OK | 235 | ||
| macos-oldrel | OK | 283 | ||
| windows-devel | OK | 171 | ||
| windows-release | OK | 199 | ||
| windows-oldrel | OK | 169 | ||
| wasm-release | OK | 156 |
Exports:addCustomAnnotbuildDrugAgeDBdbxml2dfdefaultAnnotdeleteAnnotdf2SQLitelistAnnotloadAnnotloadSDFwithNameprocessDrugagequeryAnnotDB
Dependencies:AnnotationDbiAnnotationHubaskpassbase64encBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocManagerBiocVersionBiostringsbitbit64bitopsblobbslibcachemChemmineRclicpp11crayoncrosstalkcurlDBIdbplyrdigestdplyrDTevaluatefarverfastmapfilelockfontawesomefsgenericsggplot2gluegridExtragtablehighrhtmltoolshtmlwidgetshttrhttr2IRangesisobandjquerylibjsonliteKEGGRESTknitrlabelinglaterlazyevallifecyclemagrittrmemoisemimeopensslotelpillarpkgconfigpngpromisespurrrR6rappdirsRColorBrewerRcppRCurlrjsonrlangrmarkdownRSQLitersvgS4VectorsS7sassscalesSeqinfostringistringrsystibbletidyrtidyselecttinytexutf8vctrsviridisLitewithrxfunXMLXVectoryaml
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 |