Interactive And Collaborative Exploration Of Large-Scale Transcriptomics Data With

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# Interactive And Collaborative Exploration Of Large-Scale Transcriptomics Data With <a href="https://bioconductor.org/packages/iSEE/"><img src="img/isee-sticker.png" alt="logo" style="vertical-align:bottom" height="70px"></a>
## CCB talk 2021
### <i class="fab fa-github" style="color: #000000;"></i> <a href="https://kevinrue.github.io">kevinrue</a> <i class="fab fa-twitter" style="color: #1da1f2;"></i> <a href="https://twitter.com/KevinRUE67">KevinRUE67</a> <i class="fab fa-linkedin" style="color: #0e76a8;"></i> <a href="https://www.linkedin.com/in/kevin-rue-albrecht/">kevin-rue-albrecht</a>
### Kevin Rue-Albrecht, Sims Group
### 2021-11-05

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<div class="my-footer"><span>
Interactive And Collaborative Exploration Of Large-Scale Transcriptomics Data With iSEE
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# iSEE

![](img/pbmc3k-prettified.png)

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# <svg aria-hidden="true" role="img" viewBox="0 0 512 512" style="height:1em;width:1em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:currentColor;overflow:visible;position:static;"><path d="M223.75 130.75L154.62 15.54A31.997 31.997 0 0 0 127.18 0H16.03C3.08 0-4.5 14.57 2.92 25.18l111.27 158.96c29.72-27.77 67.52-46.83 109.56-53.39zM495.97 0H384.82c-11.24 0-21.66 5.9-27.44 15.54l-69.13 115.21c42.04 6.56 79.84 25.62 109.56 53.38L509.08 25.18C516.5 14.57 508.92 0 495.97 0zM256 160c-97.2 0-176 78.8-176 176s78.8 176 176 176 176-78.8 176-176-78.8-176-176-176zm92.52 157.26l-37.93 36.96 8.97 52.22c1.6 9.36-8.26 16.51-16.65 12.09L256 393.88l-46.9 24.65c-8.4 4.45-18.25-2.74-16.65-12.09l8.97-52.22-37.93-36.96c-6.82-6.64-3.05-18.23 6.35-19.59l52.43-7.64 23.43-47.52c2.11-4.28 6.19-6.39 10.28-6.39 4.11 0 8.22 2.14 10.33 6.39l23.43 47.52 52.43 7.64c9.4 1.36 13.17 12.95 6.35 19.59z"/></svg> Winners of the 1st RStudio Shiny Contest

.center[
_"Most technically impressive"_
]

.footnote[
Read more: <https://blog.rstudio.com/2019/04/05/first-shiny-contest-winners/>
]

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# <i class="fas fa-users"></i> Team effort

<br/>

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

.center[
<a href="https://bioconductor.org/">
<img src="img/bioconductor-sticker.png" alt="iSEE" height="200px">
</a>
<a href="https://bioconductor.github.io/EuroBioc2017/">
<img src="img/EuroBioc2017-sticker.png" alt="iSEE" height="200px">
</a>
]

---

# Bioconductor

.pull-left[
## Release 3.13 (April 2021)

- 2042 software packages
- 406 experiment data packages
- 965 annotation packages
- 29 workflows

<https://bioconductor.org/>

.center[
<img src="img/bioconductor-sticker.png" alt="iSEE" height="200px">
]
]

.pull-right[
<img src="img/osca.fig3.workflow.png" height="450px" />

.small-p[
[Orchestrating single-cell analysis with Bioconductor](https://doi.org/10.1038/s41592-019-0700-8)
<a name=cite-amezquita2020osca></a>([Amezquita, Lun, Becht, et al., 2020](https://www.ncbi.nlm.nih.gov/pubmed/31792435))
]
]

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# SingleCellExperiment

![](img/osca.fig2.sce.png)

.small-p[
[Orchestrating single-cell analysis with Bioconductor](https://doi.org/10.1038/s41592-019-0700-8)
([Amezquita, Lun, Becht, et al., 2020](https://www.ncbi.nlm.nih.gov/pubmed/31792435))
]

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# SingleCellExperiment & iSEE

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# Parameter boxes

![](img/pbmc3k-parametes-boxes.png)

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# Transmitted selections

![](img/pbmc3k-selection.png)

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# Code tracker

![](img/pbmc3k-code-tracker.png)

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# Panel settings

![](img/pbmc3k-panel-settings.png)

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# Preconfigured applications

.pull-left[
## Define the initial state

```r
initial <- list(
    ReducedDimensionPlot(
        PanelWidth = 6L,
        Type = "TSNE",
        ColorByColumnData = "Cluster"
    )
)
```
]

.pull-right[
## Alternatively

Use the panel settings exported from a past session.
]

## Configure the app and launch!

```r
app <- iSEE(pbmc3k, initial = initial)
shiny::runApp(app)
```

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# Guided tours

![](img/allen-tour.png)

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# Developing new panels

![](img/panel-classes.png)

.right[
`AggregatedDotPlot`, `DynamicMarkerTable`, `DynamicReducedDimensionPlot`, ...
<a href="https://bioconductor.org/packages/iSEEu/">
<img src="img/iseeu-sticker.png" alt="logo" style="vertical-align:middle" height="80px">
</a>
]

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# Custom landing pages

![](img/landing-page.png)

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# More

- Not only single-cell transcriptomics, but any rectangular experimental data set, e.g.
  
  + bulk assays (e.g., RNA-seq, ChIP-seq)

+ microarray
  
  + flow cytometry
  
  + ...

<br/>

- Voice recognition, with `iSEE(..., voice = TRUE)`

<br/>

- Online book [Extending iSEE](https://isee.github.io/iSEE-book/)

---

# References

.small-text[
<a name=bib-amezquita2020osca></a>[Amezquita, R. A., A. T. L. Lun, E.
Becht, et al.](#cite-amezquita2020osca) (2020). "Orchestrating
single-cell analysis with Bioconductor". In: _Nat Methods_ 17.2, pp.
137-145. ISSN: 1548-7105 (Electronic) 1548-7091 (Linking). DOI:
[10.1038/s41592-019-0654-x](https://doi.org/10.1038%2Fs41592-019-0654-x).
URL:
[https://www.ncbi.nlm.nih.gov/pubmed/31792435](https://www.ncbi.nlm.nih.gov/pubmed/31792435).

<a name=bib-rue2018isee></a>[Rue-Albrecht, K., F. Marini, C. Soneson,
et al.](#cite-rue2018isee) (2018). "iSEE: Interactive
SummarizedExperiment Explorer". In: _F1000Res_ 7, p. 741. ISSN:
2046-1402 (Print) 2046-1402 (Linking). DOI:
[10.12688/f1000research.14966.1](https://doi.org/10.12688%2Ff1000research.14966.1).
URL:
[https://www.ncbi.nlm.nih.gov/pubmed/30002819](https://www.ncbi.nlm.nih.gov/pubmed/30002819).
]

.center[
<a href="https://bioconductor.org/packages/iSEE/">
<img src="img/isee-sticker.png" alt="logo" style="vertical-align:middle" height="80px">
</a>
]

---

# Other projects & commitments

- [OBDS Training Programme](https://www.imm.ox.ac.uk/research/units-and-centres/mrc-wimm-centre-for-computational-biology/training/oxford-biomedical-data-science-training-programme)

- Software development & maintenance

+ <a href="https://github.com/kevinrue/velociraptor">
  <img src="img/velociraptor-sticker.png" alt="logo" style="vertical-align:middle"   height="80px">
  </a>
  <a href="https://github.com/iSEE/iSEEu">
  <img src="img/iseeu-sticker.png" alt="logo" style="vertical-align:middle"   height="80px">
  </a>
  <a href="https://github.com/iSEE/iSEE">
  <img src="img/isee-sticker.png" alt="logo" style="vertical-align:middle"   height="80px">
  </a>
  <a href="https://github.com/kevinrue/TVTB">
  <img src="img/tvtb-sticker.png" alt="logo" style="vertical-align:middle"   height="80px">
  </a>
  <a href="https://github.com/kevinrue/GOexpress">
  <img src="img/goexpress-sticker.png" alt="logo" style="vertical-align:middle"   height="80px">
  </a>

+ [CapCruncher](https://github.com/sims-lab/CapCruncher): Analysis software for Capture-C, Tri-C and Tiled-C data

- Member of the [Biocondutor Community Advisory Board](http://www.bioconductor.org/about/community-advisory-board/)

+ Multilingual Code of Conduct: <https://github.com/kevinrue/bioc_coc_multilingual>

+ Education Committe - The Carpentries lesson development: [The Bioconductor project](https://github.com/carpentries-incubator/bioc-project)

+ Online book: [Bioconductor Packages: Development, Maintenance, and Peer Review](http://contributions.bioconductor.org/)
  
  + Online materials: [Bioconductor Guidelines for Mentors and Mentees](https://kevinrue.github.io/bioc-mentorship-docs/)
  
- Conference talk: [NextGen Omics UK 2021](https://www.oxfordglobal.co.uk/nextgen-omics-series-uk/) (November 4-5 & 8, 2021)