first.qmd

# First use

## Quick start

The [*iSEE*][bioc-isee] package is built around the `iSEE()` function.

In the simplest case, given nothing more than a [*SummarizedExperiment*][bioc-summarizedexperiment] object, the `iSEE()` function automatically scans the object for information stored in standard components and returns a shiny app object.
If the shiny app object is not assigned to an object name, the app is immediately launched in a new window.

The code chunk below illustrate *conceptually* how:

- Packages are attached to the *R* session.
- A [*SummarizedExperiment*][bioc-summarizedexperiment] object is produced.
- A [*SummarizedExperiment*][bioc-summarizedexperiment] object is given to the `iSEE()` function.

```r
library(SummarizedExperiment)
library(iSEE)
se <- SummarizedExperiment(...)
iSEE(se)
```

::: {.callout-warning}
In the code chunk above, `SummarizedExperiment(...)` is pseudo-code that *represents* the creation of a [*SummarizedExperiment*][bioc-summarizedexperiment] object; do not run that code!
In practice, you will produce those objects through your own scripts and workflows.
:::

[bioc-isee]: https://bioconductor.org/packages/iSEE/
[bioc-summarizedexperiment]: https://bioconductor.org/packages/release/bioc/html/SummarizedExperiment.html