tidysbml
This is the development version of tidysbml; for the stable release version, see tidysbml.
Extract SBML's data into dataframes
Bioconductor version: Development (3.24)
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]
, Christine Nardini [aut]
Maintainer: Veronica Paparozzi <veronicapaparozzi1 at gmail.com>
citation("tidysbml")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("tidysbml")
For older versions of R, please refer to the appropriate Bioconductor 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 | 1.7.0 |
| In Bioconductor since | BioC 3.20 (R-4.4) (2 years) |
| 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
Follow Installation instructions to use this package in your R session.
| Source Package | tidysbml_1.7.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | tidysbml_1.7.0.tgz |
| macOS Binary (sonoma-arm64) | tidysbml_1.7.0.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 |