1 Introduction

iSEEhub is an extension to the iSEE Bioconductor package that provides a link between iSEE and the Bioconductor ExperimentHub.

Specifically, iSEEhub adds a custom landing page to iSEE web applications that can be used to browse the Bioconductor ExperimentHub interactively, and loads a selected data set in the standard iSEE user interface.

2 Basics

2.1 Install iSEEhub

R is an open-source statistical environment which can be easily modified to enhance its functionality via packages. iSEEhub is a R package available via the Bioconductor repository for packages. R can be installed on any operating system from CRAN after which you can install iSEEhub by using the following commands in your R session:

if (!requireNamespace("BiocManager", quietly = TRUE)) {
      install.packages("BiocManager")
  }

BiocManager::install("iSEEhub")

## Check that you have a valid Bioconductor installation
BiocManager::valid()

2.2 Required knowledge

iSEEhub is based on many other packages that have implemented the infrastructure needed for dealing with omics data and interactive visualisation. That is, packages like SummarizedExperiment, SingleCellExperiment, iSEE and shiny.

If you are asking yourself the question “Where do I start using Bioconductor?” you might be interested in this blog post.

2.3 Asking for help

As package developers, we try to explain clearly how to use our packages and in which order to use the functions. But R and Bioconductor have a steep learning curve so it is critical to learn where to ask for help. The blog post quoted above mentions some but we would like to highlight the Bioconductor support site as the main resource for getting help: remember to use the iSEEhub tag and check the older posts. Other alternatives are available such as creating GitHub issues and tweeting. However, please note that if you want to receive help you should adhere to the posting guidelines. It is particularly critical that you provide a small reproducible example and your session information so package developers can track down the source of the error.

2.4 Citing iSEEhub

We hope that iSEEhub will be useful for your research. Please use the following information to cite the package and the overall approach. Thank you!

## Citation info
citation("iSEEhub")
#> To cite package 'iSEEhub' in publications use:
#> 
#>   Rue-Albrecht K (2024). _iSEEhub: iSEE for the Bioconductor ExperimentHub_. R package version 1.7.0,
#>   <https://github.com/iSEE/iSEEhub>.
#> 
#> A BibTeX entry for LaTeX users is
#> 
#>   @Manual{,
#>     title = {iSEEhub: iSEE for the Bioconductor ExperimentHub},
#>     author = {Kevin Rue-Albrecht},
#>     year = {2024},
#>     note = {R package version 1.7.0},
#>     url = {https://github.com/iSEE/iSEEhub},
#>   }

Here is an example of you can cite your package inside the vignette:

3 Quick start to using to iSEEhub

The main functionality of the package is available through the function iSEEhub().

The function returns a shiny app that can then be launched using the function shiny::runApp().

library(iSEEhub)
library(ExperimentHub)
ehub <- ExperimentHub()

app <- iSEEhub(ehub)

if (interactive()) {
  shiny::runApp(app, port = 1234)
}