Introduction | Installation | Sets | Which column a software version reports | The data of a result | The same code for every software | Several sets and qualifiers | Sets an app or an annotation answers | Requirements | Rule coverage | A newer catalog | Session information
Package: apbCatalogR 0.99.4
Witek Wolski
apbCatalogR: Look Up APB Result Fields by Meaning
Looks up the fields of AnnData Proteomics Bridge (APB) results by meaning, such as a PEP or an unnormalized intensity, without naming vendor columns. Reimplements the apb-catalog API on the bundle apb-catalog releases: reviewed sets, apb2's rule levels and expected answers. Reads APB results, as h5ad, Parquet or DuckDB, into anndataR objects.
Authors:
apbCatalogR_0.99.4.tar.gz
apbCatalogR_0.99.4.zip(r-4.7-any)apbCatalogR_0.99.4.zip(r-4.6-any)apbCatalogR_0.99.4.zip(r-4.5-any)
apbCatalogR_0.99.4.tgz(r-4.6-any)apbCatalogR_0.99.4.tgz(r-4.5-any)
apbCatalogR_0.99.4.tar.gz(r-4.7-any)apbCatalogR_0.99.4.tar.gz(r-4.6-any)
apbCatalogR_0.99.4.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
apbCatalogR/json (API)
| # Install 'apbCatalogR' in R: |
| install.packages('apbCatalogR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/anndata-omics-bridge/apbcatalogr/issues
Pkgdown/docs site:https://anndata-omics-bridge.github.io
proteomicsmassspectrometrydataimportinfrastructure
Last updated from:8a4daab91e. Checks:1 NOTE, 9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 183 | ||
| linux-devel | OK | 339 | ||
| source / vignettes | OK | 216 | ||
| linux-release | OK | 337 | ||
| macos-release | OK | 199 | ||
| macos-oldrel | OK | 2929 | ||
| windows-devel | OK | 2416 | ||
| windows-release | OK | 448 | ||
| windows-oldrel | OK | 2099 | ||
| wasm-release | OK | 120 |
Exports:Catalogcatalog_tablecatalog_versionDataCatalogParsedLevelsread_parsed_levelsrule_coveragesetsupdate_catalog
Dependencies:anndataRcliglueherejsonlitelatticelifecyclemagrittrMatrixpngpurrrR6rappdirsRcppRcppTOMLreticulaterlangrprojrootvctrswithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Read a var or obs slot by several keys | [.Columns |
| Read a slot by key | [[.Slot |
| Which column one software version reports for each meaning | Catalog |
| The catalog as one long table | catalog_table |
| The catalog in use | catalog_version |
| A var or obs slot, also read by several names | Columns |
| What one result's fields mean to one consumer | DataCatalog |
| One level of a result, read through a catalog | Level |
| One level of a software version's rule, holding names | LevelNames |
| One APB result: its levels on one observation axis | ParsedLevels |
| Read an APB result | read_parsed_levels |
| Check every rule against one set | rule_coverage |
| The catalog's sets | sets |
| One slot of a level, read by key first | Slot |
| Install a catalog bundle | update_catalog |