<!-- README.md is generated from README.Rmd. Please edit that file --> # iSEEindex <!-- badges: start --> [](https://github.com/iSEE/iSEEindex/issues) [](https://github.com/iSEE/iSEEindex/pulls) [](https://lifecycle.r-lib.org/articles/stages.html#experimental) [](https://github.com/iSEE/iSEEindex/actions) [](https://app.codecov.io/gh/iSEE/iSEEindex?branch=main) <!-- badges: end --> The goal of *[iSEEindex](https://bioconductor.org/packages/3.16/iSEEindex)* is to provide an interface to any collection of data sets, hosted anywhere, within a single iSEE web-application. The main functionality of this package is to define a custom landing page for iSEE web-applications where app maintainers can list entirely custom collections of data sets hosted on virtually any locally or remotely accessible network. A number of built-in methods are implemented, providing access to common types of resources, e.g.: - Local filesystem - HTTPS URIs - Amazon S3 buckets Each type of resource is identified by the scheme component of its URI. Standard schemes can be used alongside custom-made ones, e.g.: - `localhost://` for local files. - `https://` for files downloaded over the HTTPS protocol. - `s3://` for files downloaded from Amazon S3 buckets. The *[iSEEindex](https://bioconductor.org/packages/3.16/iSEEindex)* framework enables app maintainers to independently define new methods for their own choice of standard and custom-made URI schemes. More information is available in the vignette *Implementing custom iSEEindex resources*. The resulting landing page presents end-users of the web-applications with the predefined choice of data sets and initial configuration states (specific to each data set). After selecting a data set and – optionally – an initial configuration, launching the main app fetches resources from their respective URI and caches them using the *[BiocFileCache](https://bioconductor.org/packages/3.16/BiocFileCache)* package. Finally, data sets and configurations are loaded from the cache into the main `iSEE` application, for interactive exploration. ## Installation instructions Get the latest stable `R` release from [CRAN](http://cran.r-project.org/). Then install *[iSEEindex](https://bioconductor.org/packages/3.16/iSEEindex)* from [Bioconductor](http://bioconductor.org/) using the following code: ``` r if (!requireNamespace("BiocManager", quietly = TRUE)) { install.packages("BiocManager") } BiocManager::install("iSEEindex") ``` And the development version from [GitHub](https://github.com/iSEE/iSEEindex) with: ``` r BiocManager::install("iSEE/iSEEindex") ``` ## Example This is a basic example which shows you how to launch an application that lists publicly available data sets hosted on [zenodo.org](https://zenodo.org/record/7304331): ``` r library("iSEEindex") library("BiocFileCache") bfc <- BiocFileCache(cache = tempdir()) dataset_fun <- function() { x <- yaml::read_yaml(system.file(package = "iSEEindex", "example.yaml")) x$datasets } initial_fun <- function() { x <- yaml::read_yaml(system.file(package = "iSEEindex", "example.yaml")) x$initial } app <- iSEEindex(bfc, dataset_fun, initial_fun) if (interactive()) { shiny::runApp(app, port = 1234) } ``` ## Citation Below is the citation output from using `citation('iSEEindex')` in R. Please run this yourself to check for any updates on how to cite **iSEEindex**. ``` r print(citation('iSEEindex'), bibtex = TRUE) #> #> To cite package 'iSEEindex' in publications use: #> #> Rue-Albrecht K (2022). _iSEEindex: iSEE extension for a landing page #> to a custom collection of data sets_. R package version 0.99.0, #> <https://github.com/iSEE/iSEEindex>. #> #> A BibTeX entry for LaTeX users is #> #> @Manual{, #> title = {iSEEindex: iSEE extension for a landing page to a custom collection of data sets}, #> author = {Kevin Rue-Albrecht}, #> year = {2022}, #> note = {R package version 0.99.0}, #> url = {https://github.com/iSEE/iSEEindex}, #> } ``` Please note that the *[iSEEindex](https://bioconductor.org/packages/3.16/iSEEindex)* 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 *[iSEEindex](https://bioconductor.org/packages/3.16/iSEEindex)* 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/iSEEindex) 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)*. <!-- Links -->