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# iSEEhub
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The goal of `iSEEhub` is to provide an interface to the Bioconductor
*[ExperimentHub](https://bioconductor.org/packages/3.16/ExperimentHub)*
directly within an *[iSEE](https://bioconductor.org/packages/3.16/iSEE)*
web-application.
The main functionality of this package is to define a custom landing
page allowing users to browse the Bioconductor
*[ExperimentHub](https://bioconductor.org/packages/3.16/ExperimentHub)*
and directly load objects into an
*[iSEE](https://bioconductor.org/packages/3.16/iSEE)* web-application.
## Installation instructions
Get the latest stable `R` release from
[CRAN](http://cran.r-project.org/). Then install `iSEEhub` from
[Bioconductor](http://bioconductor.org/) using the following code:
``` r
if (!requireNamespace("BiocManager", quietly = TRUE)) {
install.packages("BiocManager")
}
BiocManager::install("iSEEhub")
```
And the development version from
[GitHub](https://github.com/iSEE/iSEEhub) with:
``` r
BiocManager::install("iSEE/iSEEhub")
```
## Example
This is a basic example which shows you how to solve a common problem:
``` r
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)
}
```
<img src="vignettes/screenshots/landing_page_overview.png" width="100%" />
## Citation
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**.
``` r
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.
## Code of Conduct
Please note that the `iSEEhub` project is released with a [Contributor
Code of Conduct](http://bioconductor.org/about/code-of-conduct/). By
contributing to this project, you agree to abide by its terms.
## Development tools
- Continuous code testing is possible thanks to [GitHub
actions](https://www.tidyverse.org/blog/2020/04/usethis-1-6-0/)
through *[usethis](https://CRAN.R-project.org/package=usethis)*,
*[remotes](https://CRAN.R-project.org/package=remotes)*, and
*[rcmdcheck](https://CRAN.R-project.org/package=rcmdcheck)*
customized to use [Bioconductor’s docker
containers](https://www.bioconductor.org/help/docker/) and
*[BiocCheck](https://bioconductor.org/packages/3.16/BiocCheck)*.
- Code coverage assessment is possible thanks to
[codecov](https://codecov.io/gh) and
*[covr](https://CRAN.R-project.org/package=covr)*.
- The [documentation website](http://isee.github.io/iSEEhub) is
automatically updated thanks to
*[pkgdown](https://CRAN.R-project.org/package=pkgdown)*.
- The code is styled automatically thanks to
*[styler](https://CRAN.R-project.org/package=styler)*.
- The documentation is formatted thanks to
*[devtools](https://CRAN.R-project.org/package=devtools)* and
*[roxygen2](https://CRAN.R-project.org/package=roxygen2)*.
For more details, check the `dev` directory.
This package was developed using
*[biocthis](https://bioconductor.org/packages/3.16/biocthis)*.
## Code of Conduct
Please note that the iSEEhub project is released with a [Contributor
Code of Conduct](http://bioconductor.org/about/code-of-conduct/). By
contributing to this project, you agree to abide by its terms.
