iSEE workshop - package and functionality

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# iSEE workshop - package and functionality
## European Bioconductor Meeting 2020
### <a href="https://csoneson.github.io">Charlotte Soneson</a>, <a href="https://kevinrue.github.io">Kevin Rue-Albrecht</a>, <a href="https://federicomarini.github.io/">Federico Marini</a>, <a href="https://orcid.org/0000-0002-3564-4813/">Aaron Lun</a>
### 2020-12-16 (updated: 2020-12-17)

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<div class="my-footer"><span>
iSEE Workshop 2020
&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;
interactive SummarizedExperiment Explorer
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# Structure of the session

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## Timeline

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This session is 90 minutes.

- Introduction slides

- Cloud workshop setup

- Introduction to the GUI

- Interactive exercises
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## Interact

<i class="fab fa-slack"></i> Slack [#isee](https://community-bioc.slack.com/archives/C8BJLSP8T)

<i class="fab fa-github-square"></i> Slides [GitHub Pages](https://isee.github.io/iSEEWorkshopEuroBioc2020Slides/#1)

<i class="fab fa-github-square"></i> Workshop vignette [GitHub Pages](https://isee.github.io/iSEEWorkshopEuroBioc2020)

<i class="fab fa-github"></i>
GitHub [organization](https://github.com/iSEE)
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# <i class="fas fa-users"></i> The team

<br/>

<table>
<tr>
<td width="25%"><a href="https://kevinrue.github.io"><img src="img/people/kevin-rue.jpg"></a></td>
<td width="25%"><a href="https://csoneson.github.io"><img src="img/people/charlotte-soneson.png"></a></td>
<td width="25%"><a href="https://federicomarini.github.io"><img src="img/people/federico-marini.png"></a></td>
<td width="25%"><a href="https://orcid.org/0000-0002-3564-4813"><img src="img/people/aaron-lun.png"></a></td>
</tr>
<tr>
<td align='center' width="25%">Kevin</td>
<td align='center' width="25%">Charlotte</td>
<td align='center' width="25%">Federico</td>
<td align='center' width="25%">Aaron</td>
</tr>
</table>

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This was a team effort!

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# <i class="fas fa-pencil-ruler"></i> Designed for Bioconductor

<https://bioconductor.org>

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iSEE tightly integrates with other packages of the Bioconductor project.

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# SingleCellExperiment

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]

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iSEE focuses on the SingleCellExperiment class.
This class stores all the data and metadata associated with assays, cells, and features.

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# SingleCellExperiment usage in a workflow

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- Data import (`DropletUtils`, `tximeta`)

- Quality control (`scater`)

- Normalization, feature selection (`scran`, `zinbwave`)

- Dimensionality reduction (`BiocSingular`, `scater`, `zinbwave`)

- Clustering (`SC3`, `clustree`)

- Marker gene detection (`scran`, `scDD`)

- Trajectory inference (`slingshot`)

- Visualization (`iSEE`)

- And much more...
]

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<img src="img/OSCA/bioc-figures_v2-03.png" width="1960" style="display: block; margin: auto;" />

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The SingleCellExperiment class is designed to accomodate all the information produced along a typical single-cell analysis workflow.

Those data include raw data:

- raw assay data
- experimental metadata
Processed data:
- quality control metrics
- normalized data
- dimensionality reduction results
Downstream analyses:
- cluster labels
- differential expression results
- downstream cell and feature annotations

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# iSEE <i class="fas fa-heartbeat"></i> SingleCellExperiment

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]

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Here we demonstrate how iSEE dissects SCE objects to produce figures.

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# The iSEE interface

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iSEE provides a powerful yet flexible user interface that includes 8 predefined panel types.
That said, it also gives the freedom to define any number custom panel types, both plots and tables.

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# <i class="fas fa-laptop"></i> Workshop

## To get started

- Log in to [http://app.orchestra.cancerdatasci.org/](http://app.orchestra.cancerdatasci.org/)

- Choose the `iSEE: Interactive SummarizedExperiment Explorer` workshop and launch the RStudio session

- In a separate tab, open the [pkgdown website](https://isee.github.io/iSEEWorkshopEuroBioc2020/) - vignettes are available under 'Articles'

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With that introduction to the user interface, let us head into the workshop!

Generated by: <i class="fab fa-github"></i> [kevinrue/magick-profile](https://github.com/kevinrue/magick-profile)

- [Interface overview](https://isee.github.io/iSEEWorkshopEuroBioc2020/articles/overview.html),
  or `vignette('overview', 'iSEEWorkshopEuroBioc2020')`

- [Exercises/"recipes"](https://isee.github.io/iSEEWorkshopEuroBioc2020/articles/recipes.html),
  or, `vignette('recipes', 'iSEEWorkshopEuroBioc2020')`