The goal of iSEEhub is to provide an interface to the Bioconductor
ExperimentHub
directly within an iSEE
web-application.
The main functionality of this package is to define a custom landing page allowing users to browse the Bioconductor ExperimentHub and directly load objects into an iSEE web-application.
Get the latest stable R release from
CRAN. Then install iSEEhub from
Bioconductor using the following code:
if (!requireNamespace("BiocManager", quietly = TRUE)) {
install.packages("BiocManager")
}
BiocManager::install("iSEEhub")And the development version from GitHub with:
BiocManager::install("iSEE/iSEEhub")This is a basic example which shows you how to solve a common problem:
library("iSEEhub")
#> Warning: package 'BiocGenerics' was built under R version 4.2.1
#> Warning: package 'GenomeInfoDb' was built under R version 4.2.1
library(ExperimentHub)
ehub <- ExperimentHub()
app <- iSEEhub(ehub)
if (interactive()) {
shiny::runApp(app, port = 1234)
}
Below is the citation output from using citation('iSEEhub') in R.
Please run this yourself to check for any updates on how to cite
iSEEhub.
print(citation('iSEEhub'), bibtex = TRUE)
#>
#> kevinrue (2022). _Demonstration of a Bioconductor Package_. doi:
#> 10.18129/B9.bioc.iSEEExperimentHub (URL:
#> https://doi.org/10.18129/B9.bioc.iSEEExperimentHub),
#> https://github.com/kevinrue/iSEEExperimentHub/iSEEExperimentHub - R
#> package version 0.99.0, <URL:
#> http://www.bioconductor.org/packages/iSEEExperimentHub>.
#>
#> A BibTeX entry for LaTeX users is
#>
#> @Manual{,
#> title = {Demonstration of a Bioconductor Package},
#> author = {{kevinrue}},
#> year = {2022},
#> url = {http://www.bioconductor.org/packages/iSEEExperimentHub},
#> note = {https://github.com/kevinrue/iSEEExperimentHub/iSEEExperimentHub - R package version 0.99.0},
#> doi = {10.18129/B9.bioc.iSEEExperimentHub},
#> }
#>
#> kevinrue (2022). "Demonstration of a Bioconductor Package." _bioRxiv_.
#> doi: 10.1101/TODO (URL: https://doi.org/10.1101/TODO), <URL:
#> https://www.biorxiv.org/content/10.1101/TODO>.
#>
#> A BibTeX entry for LaTeX users is
#>
#> @Article{,
#> title = {Demonstration of a Bioconductor Package},
#> author = {{kevinrue}},
#> year = {2022},
#> journal = {bioRxiv},
#> doi = {10.1101/TODO},
#> url = {https://www.biorxiv.org/content/10.1101/TODO},
#> }Please note that the iSEEhub was only made possible thanks to many
other R and bioinformatics software authors, which are cited either in
the vignettes and/or the paper(s) describing this package.
Please note that the iSEEhub project is released with a Contributor
Code of Conduct. By
contributing to this project, you agree to abide by its terms.
- Continuous code testing is possible thanks to GitHub actions through usethis, remotes, and rcmdcheck customized to use Bioconductor’s docker containers and BiocCheck.
- Code coverage assessment is possible thanks to codecov and covr.
- The documentation website is automatically updated thanks to pkgdown.
- The code is styled automatically thanks to styler.
- The documentation is formatted thanks to devtools and roxygen2.
For more details, check the dev directory.
This package was developed using biocthis.
Please note that the iSEEhub project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.