Package: bugsigdbr 1.13.0
Ludwig Geistlinger
bugsigdbr: R-side access to published microbial signatures from BugSigDB
The bugsigdbr package implements convenient access to bugsigdb.org from within R/Bioconductor. The goal of the package is to facilitate import of BugSigDB data into R/Bioconductor, provide utilities for extracting microbe signatures, and enable export of the extracted signatures to plain text files in standard file formats such as GMT.
Authors:
bugsigdbr_1.13.0.tar.gz
bugsigdbr_1.13.0.zip(r-4.5)bugsigdbr_1.13.0.zip(r-4.4)bugsigdbr_1.13.0.zip(r-4.3)
bugsigdbr_1.13.0.tgz(r-4.4-any)bugsigdbr_1.13.0.tgz(r-4.3-any)
bugsigdbr_1.13.0.tar.gz(r-4.5-noble)bugsigdbr_1.13.0.tar.gz(r-4.4-noble)
bugsigdbr_1.13.0.tgz(r-4.4-emscripten)bugsigdbr_1.13.0.tgz(r-4.3-emscripten)
bugsigdbr.pdf |bugsigdbr.html✨
bugsigdbr/json (API)
NEWS
| # Install 'bugsigdbr' in R: |
| install.packages('bugsigdbr', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/waldronlab/bugsigdbr/issues
On BioConductor:bugsigdbr-1.13.0(bioc 3.21)bugsigdbr-1.12.0(bioc 3.20)
dataimportgenesetenrichmentmetagenomicsmicrobiomebioconductor-package
Last updated 2 months agofrom:3d187dcdb8. Checks:OK: 1 NOTE: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 29 2024 |
| R-4.5-win | NOTE | Nov 29 2024 |
| R-4.5-linux | NOTE | Nov 29 2024 |
| R-4.4-win | NOTE | Nov 29 2024 |
| R-4.4-mac | NOTE | Nov 29 2024 |
| R-4.3-win | NOTE | Nov 29 2024 |
| R-4.3-mac | NOTE | Nov 29 2024 |
Exports:browseSignaturebrowseTaxonextractTaxLevelgetMetaSignaturesgetOntologygetSignaturesimportBugSigDBrestrictTaxLevelsubsetByOntologywriteGMT
Dependencies:askpassBiocFileCachebitbit64blobcachemclicpp11crayoncurlDBIdbplyrdplyrfansifastmapfilelockgenericsgluehmshttrjsonlitelifecyclemagrittrmemoisemimeopensslpillarpkgconfigplogrprettyunitsprogresspurrrR6rlangRSQLitestringistringrsystibbletidyrtidyselecttzdbutf8vctrsvroomwithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Displaying BugSigDB signatures pages in a web browser | browseSignature |
| Displaying BugSigDB taxon pages in a web browser | browseTaxon |
| Extract specific taxonomic levels from a microbe signature | extractTaxLevel |
| Obtain meta-signatures for a column of interest | getMetaSignatures |
| Obtain the EFO and UBERON ontology | getOntology |
| Obtain microbe signatures from BugSigDB | getSignatures |
| Obtain published microbial signatures from bugsigdb.org | importBugSigDB |
| Restrict microbe signatures to specific taxonomic levels | restrictTaxLevel |
| Ontology-based subsetting of BugSigDB signatures | subsetByOntology |
| Write microbe signatures to file in GMT format | writeGMT |
