Introduction | Where the resources are stored | Inspecting resources without downloading | Retrieving a resource | Retrieving a coherent bundle | Working from a staged directory | The three-package workflow | Recording the version used | Session information
Package: SpaMTPdb 0.99.4
Tianyao Lu
SpaMTPdb: Versioned Annotation Resources for SpaMTP
Provides lightweight, version-aware access to the annotation resources used by SpaMTP. Resources include pruned RaMP chemical, identifier, pathway, and pathway-topology tables, precomputed SMILES functional-group and ionisation features, and legacy metabolite reference tables, plus a separately versioned human gene identifier reference from fixed HGNC archives. RaMP resource files are hosted on Zenodo and described by AnnotationHub metadata rather than bundled in the package. Retrieved files are verified against recorded sizes and checksums and cached for reuse, and a local resource directory can be used for development and reproducible database builds. Maintainer recipes coordinate a shared Zenodo resource collection with SpaMTPData while preserving separate annotation and experiment registries and independent resource versions.
Authors:
SpaMTPdb_0.99.4.tar.gz
SpaMTPdb_0.99.4.zip(r-4.7-any)SpaMTPdb_0.99.4.zip(r-4.6-any)SpaMTPdb_0.99.4.zip(r-4.5-any)
SpaMTPdb_0.99.4.tgz(r-4.6-any)SpaMTPdb_0.99.4.tgz(r-4.5-any)
SpaMTPdb_0.99.4.tar.gz(r-4.7-any)SpaMTPdb_0.99.4.tar.gz(r-4.6-any)
SpaMTPdb_0.99.4.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
SpaMTPdb/json (API)
| # Install 'SpaMTPdb' in R: |
| install.packages('SpaMTPdb', repos = c('https://biocstaging.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/bcrl-tylu/spamtpdb/issues
Last updated from:a004d18957. Checks:1 NOTE, 9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 195 | ||
| linux-devel | OK | 256 | ||
| source / vignettes | OK | 242 | ||
| linux-release | OK | 200 | ||
| macos-release | OK | 179 | ||
| macos-oldrel | OK | 130 | ||
| windows-devel | OK | 158 | ||
| windows-release | OK | 158 | ||
| windows-oldrel | OK | 163 | ||
| wasm-release | OK | 160 |
Exports:spaMTPdbBundlespaMTPdbGeneReferencespaMTPdbResourcespaMTPdbResourcesspaMTPdbVersion
Dependencies:AnnotationDbiAnnotationHubaskpassBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocManagerBiocVersionBiostringsbitbit64blobcachemclicpp11crayoncurlDBIdbplyrdplyrfastmapfilelockgenericsgluehttrhttr2IRangesjsonliteKEGGRESTlifecyclemagrittrmemoisemimeopensslpillarpkgconfigpngpurrrR6rappdirsrlangRSQLiteS4VectorsSeqinfostringistringrsystibbletidyrtidyselectutf8vctrswithrXVectoryaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Retrieve a coherent set of SpaMTP annotation resources | spaMTPdbBundle |
| Retrieve a versioned human gene identifier reference | spaMTPdbGeneReference |
| Retrieve one SpaMTP annotation resource | spaMTPdbResource |
| List SpaMTPdb resources | spaMTPdbResources |
| Report the available SpaMTPdb versions | spaMTPdbVersion |
