Installation | General dataframes structure | Converting SBML into a R list | Converting SBML into dataframes | Integration with Bioconductor packages | Session info | References
Package: tidysbml 1.6.0
Veronica Paparozzi
tidysbml: Extract SBML's data into dataframes
Starting from one SBML file, it extracts information from each listOfCompartments, listOfSpecies and listOfReactions element by saving them into data frames. Each table provides one row for each entity (i.e. either compartment, species, reaction or speciesReference) and one set of columns for the attributes, one column for the content of the 'notes' subelement and one set of columns for the content of the 'annotation' subelement.
Authors:
tidysbml_1.6.0.tar.gz
tidysbml_1.6.0.zip(r-4.7-any)tidysbml_1.6.0.zip(r-4.6-any)tidysbml_1.6.0.zip(r-4.5-any)
tidysbml_1.6.0.tgz(r-4.6-any)tidysbml_1.6.0.tgz(r-4.5-any)
tidysbml_1.6.0.tar.gz(r-4.7-any)tidysbml_1.6.0.tar.gz(r-4.6-any)
tidysbml_1.6.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
tidysbml/json (API)
| # Install 'tidysbml' in R: |
| install.packages('tidysbml', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/veronicapaparozzi/tidysbml/issues
On BioConductor:tidysbml-1.7.0(bioc 3.24)tidysbml-1.6.0(bioc 3.23)
graphandnetworknetworkpathwayssoftware
Last updated from:17cdb8b3fe (on RELEASE_3_23). Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: no.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 158 | ||
| linux-devel-x86_64 | NOTE | 205 | ||
| source / vignettes | OK | 269 | ||
| linux-release-x86_64 | NOTE | 210 | ||
| macos-release-arm64 | NOTE | 81 | ||
| macos-oldrel-arm64 | NOTE | 96 | ||
| windows-devel-x86_64 | NOTE | 77 | ||
| windows-release-x86_64 | NOTE | 94 | ||
| windows-oldrel-x86_64 | NOTE | 78 | ||
| wasm-release | OK | 131 |
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Create a dataframe for the type of entity selected | as_df |
| Create a list of dataframes (full extraction) | as_dfs |
| Create R list from sbml file | sbml_as_list |
| Validate SBML schema | sbml_validate |
