class: center, middle, title-slide # <code>GeneTonic</code>: enjoy RNA-seq data analysis, responsibly ### Federico Marini (<a href="mailto:marinif@uni-mainz.de" class="email">marinif@uni-mainz.de</a>)</br> ### <p>2020/06/17<br><code>e-Rum2020</code><br><br><a href="https://bit.ly/genetonic-erum"><code>https://bit.ly/genetonic-erum</code></a><br> <code><i class="fab fa-twitter "></i> @FedeBioinfo</code></p> --- layout: true <div class="my-footer"> <span>                                  <!--            -->       <!-- <a href="http://bit.ly/genetonic2019"><code>http://bit.ly/genetonic2019</code></a> --> <a href="https://federicomarini.github.io/eRum2020"><code>https://federicomarini.github.io/eRum2020</code></a> </span> </div> --- <!-- Submitted abstract: --> <!-- GeneTonic: enjoy RNA-seq data analysis, responsibly --> <!-- GeneTonic: combining components of transcriptome analyses for efficient exploration --> <!-- Interpreting the results from RNA-seq transcriptome experiments can be a complex task, where the essential information is distributed among different tabular and list formats - normalized expression values, results from differential expression analysis, and results from functional enrichment analyses. --> <!-- The identification of relevant functional patterns, as well as their contextualization in the data and results at hand, are not straightforward operations if these pieces of information are not combined together efficiently. --> <!-- Interactivity can play an essential role in simplifying the way how one accesses and digests RNA-seq data analysis in a more comprehensive way. --> <!-- I introduce GeneTonic (https://github.com/federicomarini/GeneTonic), an application developed in Shiny and based on many essential elements of the Bioconductor project, that aims to reduce the barrier to understanding such data better, and to efficiently combine the different components of the analytic workflow. --> <!-- For example, starting from bird’s eye perspective summaries (with interactive bipartite gene-geneset graphs, or enrichment maps), it is easy to generate a number of visualizations, where drill-down user actions enable further insight and deliver additional information (e.g., gene info boxes, geneset summary, and signature heatmaps). --> <!-- Complex datasets interpretation can be wrapped up into a single call to the GeneTonic main function, which also supports built-in RMarkdown reporting, to both conclude an exploration session, or also to generate in batch the output of the available functionality, delivering an essential foundation for computational reproducibility. --> <!-- https://federicomarini.github.io/EuroBioc2019 --> <!-- Format: 8 min or so! --> <!-- Each talk has been allotted 8 minutes and presenters should aim for approximately 6 slides. The following rules will apply in these sessions in order to keep things flowing: --> <!-- There will be a warning at 7 minutes. --> <!-- At this point the next talk will be set up on the computer, allowing the next speaker to get going immediately when their time begins. --> <!-- Flashlight talks will be interrupted (possibly mid-syllable) at the 8 minute mark regardless of how many slides the speaker has left. --> <!-- I'm **Federico Marini**, Virchow Fellow @CTH Mainz/IMBEI --> <!-- I like platelets (and their transcriptome), and you should as well. --> <!-- some intro on RNA-seq --> <!-- comparison of conditions - genes, genesets, --> <!-- why is this difficult? --> <!-- analysis workflow first --> <!-- then, "what did I learn"? interdisciplinary field --> <!-- 2to tango --> <!-- non standard containers --> <!-- many tools for essential steps --> <!-- Bioc to the rescue --> <!-- spirit of interoperability --> <!-- One stop shop for interpreting RNA-seq w functional enrichment analyses & expression values integrated --> <!-- interpr: probably the real bottleneck now! --> <!-- --- --> # Transcriptomics 101 **RNA-seq** --- # Transcriptomics 101 **RNA-seq**: High dimensional snapshot to quantify the transcriptomic activity of all RNA species in a sample <!-- - Bulk or single cell? --> -- <p align="center"> <img src="images/wiki_dogma.jpg" alt="" height="400"/> </p> <!-- Quantify and compare --> --- # Transcriptomics 101 **RNA-seq**: High dimensional snapshot to quantify the transcriptomic activity of all RNA species in a sample <!-- - Bulk or single cell? --> **Data**: genes `\(\times\)` samples (e.g. bulk/single cells) **Objectives**: - Compare abundances to discover differentially expressed genes, gene signatures, etc. - features associated with phenotypic differences - Identification of cell subpopulations, description of developmental trajectories, study noise and heterogeneity in transcriptional regulation -- **A wide variety of applications exist!** <!-- different point of views, sometimes even exploiting the very same data --> --- # The analysis workflow <p align="center"> <img src="images/Interaction_nostep.png" alt=""/> </p> <p style="text-align:left;"><code><font color="green">"Hi, I am a bioinformatician!"</font> </code></p> --- # The analysis workflow <p align="center"> <img src="images/Interaction_step0.png" alt=""/> </p> <p style="text-align:right;"><code><font color="steelblue">"And I am your next collaboration parner!"</font> </code></p> --- # The analysis workflow <p align="center"> <img src="images/Interaction_step1.png" alt=""/> </p> <p style="text-align:right;"><code><font color="steelblue">"You know what, I just had a cool idea about a project..."</font> </code></p> --- # The analysis workflow <p align="center"> <img src="images/Interaction_step2.png" alt=""/> </p> <p style="text-align:left;"><code><font color="green">"Oh cool, tell me more :)"</font> </code></p> --- # The analysis workflow <p align="center"> <img src="images/Interaction_step3.png" alt=""/> </p> <p style="text-align:center;"><code><font color="coral">This was indeed a productive kickoff meeting...</font> </code></p> --- # The analysis workflow <p align="center"> <img src="images/Interaction_step4.png" alt=""/> </p> <p style="text-align:right;"><code><font color="steelblue">"I've got a couple of more questions on the data..."</font></code></p> --- # The analysis workflow <p align="center"> <img src="images/Interaction_step5.png" alt=""/> </p> <p style="text-align:right;"><code><font color="steelblue">"Well, it was more than a couple. But you can do analyses pretty quick right?"</font> </code></p> --- # The analysis workflow <p align="center"> <img src="images/Interaction_step6.png" alt=""/> </p> <p style="text-align:right;"><code><font color="steelblue">"Why don't you JUST do this tiny extra thing for me?"</font> </code></p> --- # The analysis workflow <p align="center"> <img src="images/Interaction_step7.png" alt=""/> </p> <p style="text-align:left;"><code><font color="green">"... just do it yourself?"</font> </code></p> <!-- ### *a.k.a., how do we prevent the last steps from happening?* --> <!-- Is there a better way to support these cycles of exploration, inquiry, and hypothesis generation? --> --- background-image: url("images/marie.png") background-size: cover background-position: 50% 50% class: center, bottom, inverse # Does the ~~exploration~~ interpretation of your data spark joy? --- class: center # It takes two to tango -- .huge[Results] -- ### and .huge[Interpretation] <!-- The data is **large** ("can't fit in our head") --> <!-- - use structures/containers that support alternative (out-of-memory) representations --> <!-- Our task is **complex** --> <!-- - yet we are curious and stubborn enough that we want to try and understand this --> --- class: center # It takes two to tango -- .huge[Bioinformatician] -- ### and .huge[Experimental scientist] <!-- The Pro & the Con: **We are not alone**, we work with a variety of experts --> <!-- - mind (and bridge) the gap when **communicating**! --> --- class: center # It takes two to tango -- .huge[Reproducibility] -- ### and .huge[Interactivity] <!-- # Reproducible data science = good data science --> <!-- What do you need for doing that? --> <!-- **Data** - needless to say --> <!-- **Software** - list all required packages/versions, if needed to recreate environments on demand --> <!-- **Analysis steps/parameters**, with all tools and params in each step, documenting order, inputs, outputs --> <!-- # (Interactive) Exploration and visualization: why? --> <!-- Effective and efficient methods are key to deliver... --> <!-- <i class="fas fa-check "></i> better **quality assessment** --> <!-- <i class="fas fa-check "></i> better **generation of research hypotheses** --> <!-- <i class="fas fa-check "></i> better **representation of the results** --> <!-- <i class="fas fa-check "></i> better **communication** of findings --> <!-- IMHO... (might be biased) --> <!-- - Proper analysis tools _should_ combine **interactivity and reproducibility** --> <!-- - Marini and Binder (2016) - [`10.18547/gcb.2017.vol3.iss1.e39`](https://doi.org/10.18547/gcb.2017.vol3.iss1.e39) --> <!-- - Marini and Binder (2019) - [`10.1186/s12859-019-2879-1`](https://doi.org/10.1186/s12859-019-2879-1) --> <!-- - Joe Cheng's keynote at `useR!2019` in Toulouse (welcome `shinymeta`!) --> --- class: middle, center # Bioinformaticians' best friend <p align="center"> <img src="images/Bioconductor-serial.gif" alt="" height = 250/> </p> <!-- A project, a community, a place to grow and develop software and yourself --> -- ### and Biologists' as well <!-- Essential role to cut down time in one of the best output of omics data, i.e. new questions and hypotheses --> <!-- but also: analyst and experimental scientist- gap to mind and fill --> --- # Meanwhile, on Bioconductor... <p align="center"> <img src="meanwhile_bioc/Slide1.png" alt="" height = 400/> </p> --- # Meanwhile, on Bioconductor... <p align="center"> <img src="meanwhile_bioc/Slide2.png" alt="" height = 400/> </p> [`https://www.nature.com/articles/nmeth.3252`](https://www.nature.com/articles/nmeth.3252)<br> --- # Meanwhile, on Bioconductor... <p align="center"> <img src="meanwhile_bioc/Slide3.png" alt="" height = 400/> </p> [`https://f1000research.com/articles/9-512/v1`](https://f1000research.com/articles/9-512/v1) <br>**[`https://bioconductor.org/packages/ExploreModelMatrix/`](https://bioconductor.org/packages/ExploreModelMatrix/)** --- # Meanwhile, on Bioconductor... <p align="center"> <img src="meanwhile_bioc/Slide4.png" alt="" height = 400/> </p> [`https://f1000research.com/articles/7-741/v1`](https://f1000research.com/articles/7-741/v1) <br>**[`https://bioconductor.org/packages/iSEE/`](https://bioconductor.org/packages/iSEE/)** --- # Meanwhile, on Bioconductor... <p align="center"> <img src="meanwhile_bioc/Slide5.png" alt="" height = 400/> </p> [`https://doi.org/10.1186/s13059-014-0550-8`](https://doi.org/10.1186/s13059-014-0550-8) <br>[`https://bioconductor.org/packages/DESeq2/`](https://bioconductor.org/packages/DESeq2/) --- # Meanwhile, on Bioconductor... <p align="center"> <img src="meanwhile_bioc/Slide6.png" alt="" height = 400/> </p> [`https://www.biorxiv.org/content/10.1101/2020.01.10.901652v1`](https://www.biorxiv.org/content/10.1101/2020.01.10.901652v1) <br>**[`https://bioconductor.org/packages/ideal/`](https://bioconductor.org/packages/ideal/)** --- # Meanwhile, on Bioconductor... <p align="center"> <img src="meanwhile_bioc/Slide7.png" alt="" height = 400/> </p> --- class: center # Data analysis: where's the real bottleneck? -- ✅ Efficient methods to process your data (entire workflows available, see e.g. [`https://osca.bioconductor.org/`](https://osca.bioconductor.org/)) -- ✅ Compelling ways of visualizing your data (better QC, better hypotheses, better answers `\(\rightarrow\)` see [`http://bioconductor.org/packages/iSEE/`](http://bioconductor.org/packages/iSEE/) & [`http://bioconductor.org/packages/iSEEu/`](http://bioconductor.org/packages/iSEEu/) ) -- ✅ Powerful framework to communicate, interactively and reproducibly -- 🔥 **Data interpretation** -- .pull-left[ <img src="images/thetruth.jpg" alt="" height = 200/> ] .pull-right[ <br><br><br> ... just not in plain sight ] --- class: bottom, center # Show me your data... --- background-image: url("tablestablestables/Slide1.png") background-size: contain background-position: 50% 50% class: bottom, center # Show me your data... --- background-image: url("tablestablestables/Slide2.png") background-size: contain background-position: 50% 50% class: bottom, center # Show me your data... --- background-image: url("tablestablestables/Slide3.png") background-size: contain background-position: 50% 50% class: bottom, center # Show me your data... --- background-image: url("tablestablestables/Slide4.png") background-size: contain background-position: 50% 50% class: bottom, center # Show me your data... --- background-image: url("tablestablestables/Slide5.png") background-size: contain background-position: 50% 50% class: bottom, center # Show me your data... <!-- Let the exploration of your data spark joy again --> <!-- you need combination of tables, iterations --> <!-- 4 ingredients --> <!-- (although Germans say all good things are three) --> --- class: center # A cocktail recipe <p align="center"> <img src="logocreation/logocreation_Slide1.png" alt="" height = 450/> </p> .small[*You might (and should) have a set of standardized objects for your datasets and results (Excel does __not__ count)*] --- class: center # A cocktail recipe <p align="center"> <img src="logocreation/logocreation_Slide2.png" alt="" height = 450/> </p> *A container for the expression matrix,* `dds` --- class: center # A cocktail recipe <p align="center"> <img src="logocreation/logocreation_Slide3.png" alt="" height = 450/> </p> *A container for the results of differential expression,* `res_de` --- class: center # A cocktail recipe <p align="center"> <img src="logocreation/logocreation_Slide4.png" alt="" height = 450/> </p> *A table for the result of functional enrichment,* `res_enrich` --- class: center # A cocktail recipe <p align="center"> <img src="logocreation/logocreation_Slide5.png" alt="" height = 450/> </p> *Decorate with an annotation table,* `anno_df` --- class: center # A cocktail recipe <p align="center"> <img src="logocreation/logocreation_Slide6.png" alt="" height = 450/> </p> *Shaken, not stirred...* --- class: center # A cocktail recipe <p align="center"> <img src="logocreation/logocreation_Slide7.png" alt="" height = 450/> </p> `GeneTonic` is now [on Bioconductor](https://bioconductor.org/packages/GeneTonic/)! --- background-image: url("images/tabwelcome.png") background-size: contain background-position: 50% 80% class: center ## First steps with a full glass 🍸 <!-- no need to feel overwhelmed --> --- background-image: url("images/gif_gt_welcometour.gif") background-size: contain background-position: 50% 50% class: center, bottom # --- background-image: url("images/tabgsviz_01_summary.png") background-size: contain background-position: 50% 50% class: center, bottom # Visual overviews --- background-image: url("images/tabgsviz_02_heatscores.png") background-size: contain background-position: 50% 50% class: center, bottom # --- background-image: url("images/tabgsviz_03_heatsummary.png") background-size: contain background-position: 50% 50% class: center, bottom # --- background-image: url("images/tabgsviz_04_mds.png") background-size: contain background-position: 50% 50% class: center, bottom # --- background-image: url("images/tabgsviz_05_dendro.png") background-size: contain background-position: 50% 50% class: center, bottom # --- background-image: url("images/taboverview_01_volcano.png") background-size: contain background-position: 50% 50% class: center, bottom # --- background-image: url("images/taboverview_02_tableenhanced.png") background-size: contain background-position: 50% 50% class: center, bottom # --- background-image: url("images/gif_gt_ggs.gif") background-size: contain background-position: 50% 50% class: center, bottom # The interplay of genes and genesets --- <!-- # Bringing life to enrichment --> <iframe src="visnetwork_exported_em.html" width="100%" height="80%" frameBorder="0"></iframe> ### ...bringing an enrichment map to life! --- # News from the cellar --- background-image: url("distill_concept/Slide1.png") background-size: contain background-position: 50% 50% # News from the cellar --- background-image: url("distill_concept/Slide2.png") background-size: contain background-position: 50% 50% # News from the cellar --- background-image: url("distill_concept/Slide3.png") background-size: contain background-position: 50% 50% # News from the cellar <br><br><br><br> <br><br><br><br> <br><br><br><br> <br><br><br><br> <br><br><br> `distill_table` on its way to devel! <!-- Your typical tasks: find common themes, check how they relate to the expression data, repeat. --> <!-- or better, with their efficient combination --> <!-- bird's eye perspective summaries --> <!-- info boxes --> <!-- summary vizs --> <!-- hairballs becoming info-rich with interactivity --> <!-- live demo! --> <!-- Screenshots of some functionality? --> --- # Automating things is good -- <blockquote class="twitter-tweet"> <p lang="en" dir="ltr">Accidentally duplicated every item in my <a href="https://twitter.com/zotero?ref_src=twsrc%5Etfw">@zotero</a> library.<br><br>A sane person would've written a script to automate the merging process.<br><br>I took the analogue approach. <a href="https://t.co/kAF9c6tUs3">pic.twitter.com/kAF9c6tUs3</a></p>— Dooley Murphy (@DooleyMurphy) <a href="https://twitter.com/DooleyMurphy/status/1191744575980941312?ref_src=twsrc%5Etfw">November 5, 2019</a> </blockquote> <script async src="https://platform.twitter.com/widgets.js" charset="utf-8"></script> <!-- like this like that. but after exploration, what is there? --> <!-- demo for bookmarking - with keystroke --> <!-- happy hour, works live and offline for batch processing --> <!-- will add --> <!-- from genes --> <!-- to many pathways --> <!-- to a bunch of dealable with themes --> --- background-image: url("images/tabbookmarks_01_bookmarks.png") background-size: contain background-position: 50% 50% class: center, bottom -- # Time to start the `happy_hour`! --- class: center, middle # A quick demo ```r BiocManager::install("GeneTonic") library("GeneTonic") example(GeneTonic, ask = FALSE) ``` --- background-image: url("images/GeneTonic_logo.png") background-size: 120px background-position: 90% 10% class: center # Wrapping up [`http://bioconductor.org/packages/GeneTonic/`](http://bioconductor.org/packages/GeneTonic/)<br> [<i class="fab fa-github "></i> `federicomarini/GeneTonic`](https://github.com/federicomarini/GeneTonic) -- **One stop shop** for interpreting RNA-seq with functional enrichment analyses & expression values integrated together - escape *TableLand*! -- Reducing the **time-to-generate-insight** & simplifying analysis iterations -- **Interactivity** is great and essential for making analyses accessible... -- ... never forgetting it is important to keep a **reproducible track** of the performed operations. -- Drilldown + Bookmarking & Report, in the Bioconductor spirit of **interoperability** -- Got any methods not covered yet? Let's write a `shake_` function! --- background-image: url("images/GeneTonic_logo.png") background-size: 120px background-position: 90% 10% class: center, middle ## ... thank you for your attention! You can find me here: <br> <code>marinif@uni-mainz.de - <i class="fab fa-twitter "></i></code> [`@FedeBioinfo`](https://twitter.com/FedeBioinfo)<br> <a href="https://federicomarini.github.io"><i class="fas fa-home "></i> `https://federicomarini.github.io`</a><br> <a href="http://www.imbei.de"><i class="fas fa-map-marker-alt "></i> CTH/IMBEI (Mainz, Germany)</a><br> <br><br>You can find this presentation here: <br>[`https://federicomarini.github.io/eRum2020/`](https://federicomarini.github.io/eRum2020/) [`https://bit.ly/genetonic-erum`](https://bit.ly/genetonic-erum) <br><br> ### Acknowledgements Center for Thrombosis and Hemostasis (CTH), Mainz (Virchow Fellowship) IMBEI - Biostatistics & Bioinformatics division --- <!-- empty slide -->