What can be checked | Pattern mode: is the string well-formed? | Cache mode: does the identifier exist in a snapshot? | Remote mode | Species and version awareness | HGVS variant syntax | Clean a column | Validation framework adapters | Generating test data | Summary
Package: biobouncer 0.1.0
biobouncer: Validate Biological Identifiers and Inputs
A gate for biological inputs. Validate gene symbols, ontology terms, variant formats, and database identifiers through one small API, using offline pattern and cache checks or live remote checks. Results are designed to match the companion Python package for the same inputs.
Authors:
biobouncer_0.1.0.tar.gz
biobouncer_0.1.0.zip(r-4.7)biobouncer_0.1.0.zip(r-4.6)biobouncer_0.1.0.zip(r-4.5)
biobouncer_0.1.0.tgz(r-4.6-any)biobouncer_0.1.0.tgz(r-4.5-any)
biobouncer_0.1.0.tar.gz(r-4.7-any)biobouncer_0.1.0.tar.gz(r-4.6-any)
biobouncer_0.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
biobouncer/json (API)
| # Install 'biobouncer' in R: |
| install.packages('biobouncer', repos = c('https://samuelbharti.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/samuelbharti/biobouncer/issues
Pkgdown/docs site:https://www.samuelbharti.com
Last updated from:76c0f5eac6. Checks:7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | NOTE | 140 | ||
| source / vignettes | OK | 183 | ||
| linux-release-x86_64 | NOTE | 150 | ||
| macos-release-arm64 | NOTE | 119 | ||
| macos-oldrel-arm64 | NOTE | 208 | ||
| windows-devel | NOTE | 121 | ||
| windows-release | NOTE | 134 | ||
| windows-oldrel | NOTE | 116 | ||
| wasm-release | OK | 112 |
Exports:assert_valid_idbiobouncer_cache_dirbiobouncer_pullbiobouncer_snapshotscheck_idcheck_valid_idid_predicateis_valid_idrepair_idreport_idsource_infosourcessv_biobouncersynthesize_idstest_valid_id
Dependencies:backportscheckmateclicurlgluejsonlitelifecyclemagrittrpillarpkgconfigrlangtibbleutf8vctrsyaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Assert that identifiers are valid | assert_valid_id |
| Snapshot cache directory | biobouncer_cache_dir |
| Download a snapshot for cache mode | biobouncer_pull |
| List installed snapshots | biobouncer_snapshots |
| Check biological identifiers | check_id |
| Check that identifiers are valid | check_valid_id |
| Build a vectorized predicate for data-frame validation | id_predicate |
| Test biological identifiers | is_valid_id |
| Repair a column of identifiers | repair_id |
| Validate and report on a column of identifiers | print.biobouncer_report report_id summary.biobouncer_report |
| Describe the available sources | source_info |
| List available source databases | sources |
| Create a shinyvalidate rule | sv_biobouncer |
| Generate a synthetic column of identifiers | synthesize_ids |
| Test whether identifiers are valid | test_valid_id |
