Introduction | Data schema | Analysis and Stats | Installation | Import bugphyzz data | Create microbial signatures | Run a bug set enrichment analysis | Get signatures associated with a specific microbe | Session information
Package: bugphyzz 1.7.9
Levi Waldron
bugphyzz: A harmonized data resource and software for enrichment analysis of microbial physiologies
bugphyzz is an electronic database of standardized microbial annotations. It facilitates the creation of microbial signatures based on shared attributes, which are utilized for bug set enrichment analysis. The data also includes annotations imputed with ancestra state reconstruction methods.
Authors:
bugphyzz_1.7.9.tar.gz
bugphyzz_1.7.9.tar.gz(r-4.7-any)bugphyzz_1.7.9.tar.gz(r-4.6-any)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
bugphyzz/json (API)
| # Install 'bugphyzz' in R: |
| install.packages('bugphyzz', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/waldronlab/bugphyzz/issues
On BioConductor:bugphyzz-1.7.1(data/experiment 3.24)bugphyzz-1.6.0(data/experiment 3.23)
microbiomedatareproducibleresearchr01ca230551datapkg
Last updated from:512948fe7d. Checks:1 NOTE, 3 OK. Indexed: yes.
This is a data package. Data packages may be large and do not get checked across all platforms.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 226 | ||
| linux-devel | OK | 477 | ||
| source / vignettes | OK | 455 | ||
| linux-release | OK | 296 |
Exports:getTaxonSignaturesimportBugphyzzmakeSignaturesphysiologiesshowPhys
Dependencies:askpassBiocFileCacheBiocGenericsbitbit64blobcachemclicpp11curlDBIdbplyrdigestdplyrfastmapfilelockgenericsgluehttr2lifecyclemagrittrmemoiseopensslpillarpkgconfigpurrrR6rlangRSQLiteS4Vectorsstringistringrsystibbletidyrtidyselectutf8vctrswithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Get Taxon Signatures | getTaxonSignatures |
| Import bugphyzz | importBugphyzz |
| Make signatures | makeSignatures |
| Import physiologies (for devs) | physiologies |
| Show list of available physiologies (for devs) | showPhys |