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tidysbml
This is thedevelopment version of tidysbml; for the stable release version, seetidysbml.
Extract SBML's data into dataframes
Bioconductor version: Development (3.23)
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.
Author: Veronica Paparozzi [aut, cre]
ORCID: 0009-0000-2961-1559, Christine Nardini [aut] ORCID: 0000-0001-7601-321X
Maintainer: Veronica Paparozzi <veronicapaparozzi1 at gmail.com>
citation("tidysbml")):Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")# The following initializes usage of Bioc develBiocManager::install(version='devel')BiocManager::install("tidysbml")For older versions of R, please refer to the appropriateBioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("tidysbml")| Introduction to the tidysbml package | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | GraphAndNetwork,Network,Pathways,Software |
| Version | 1.5.0 |
| In Bioconductor since | BioC 3.20 (R-4.4) (1 year) |
| License | CC BY 4.0 |
| Depends | R (>= 4.4.0) |
| Imports | xml2, methods |
| System Requirements | |
| URL | https://github.com/veronicapaparozzi/tidysbml |
| Bug Reports | https://github.com/veronicapaparozzi/tidysbml/issues |
See More
| Suggests | rmarkdown,knitr,BiocStyle,biomaRt,RCy3,testthat (>= 3.0.0) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
FollowInstallation instructions to use this package in your R session.
| Source Package | tidysbml_1.5.0.tar.gz |
| Windows Binary (x86_64) | tidysbml_1.5.0.zip |
| macOS Binary (x86_64) | tidysbml_1.5.0.tgz |
| macOS Binary (arm64) | tidysbml_1.5.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/tidysbml |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/tidysbml |
| Bioc Package Browser | https://code.bioconductor.org/browse/tidysbml/ |
| Package Short Url | https://bioconductor.org/packages/tidysbml/ |
| Package Downloads Report | Download Stats |