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microbiome · Nov 23, 2024 · 3d7d5bf · 3d7d5bf
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diff --git a/docs/hintikkaxo_presentation_files/figure-revealjs/unnamed-chunk-13-1.png b/docs/hintikkaxo_presentation_files/figure-revealjs/unnamed-chunk-13-1.png
diff --git a/docs/oma.html b/docs/oma.html
@@ -533,8 +533,15 @@ <h2>MIcrobiome Analysis (mia)</h2>
 </ul>
 
 <img data-src="images/mia_logo.png" class="quarto-figure quarto-figure-right r-stretch" style="width:10.0%" alt="mia logo."></section>
-<section id="mia-ecosystem" class="slide level2">
-<h2>mia ecosystem</h2>
+<section id="expanding-ecosystem" class="slide level2">
+<h2>Expanding ecosystem</h2>
+<div class="columns">
+<div class="column" style="width:70%;">
+<!--
+- Community-driven ecosystem of tools
+- Analysis, visualization, simulation, multi-omics, time series, ...
+- Now with a graphical user interface
+-->
 <ul>
 <li><a href="https://bioconductor.org/packages/release/bioc/html/mia.html">mia</a> (Data analysis)</li>
 <li><a href="https://bioconductor.org/packages/release/bioc/html/miaViz.html">miaViz</a> (Visualization)</li>
@@ -544,6 +551,9 @@ <h2>mia ecosystem</h2>
 <li><a href="https://bioconductor.org/packages/release/bioc/html/iSEEtree.html">iSEEtree</a> (Interactive visualization)</li>
 <li><a href="https://microbiome.github.io/OMA/docs/devel/pages/miaverse.html#sec-packages">Expanded by independent developers</a></li>
 </ul>
+</div><div class="column" style="width:30%;">
+<p><img data-src="https://raw.githubusercontent.com/microbiome/mia/refs/heads/devel/man/figures/mia_logo.png" style="width:30.0%" alt="mia logo."> <img data-src="https://raw.githubusercontent.com/EBI-Metagenomics/MGnifyR/refs/heads/devel/man/figures/mgnifyr_logo.png" style="width:30.0%" alt="MGnifyR logo."> <img data-src="https://raw.githubusercontent.com/EBI-Metagenomics/HoloFoodR/refs/heads/devel/man/figures/holofoodr_logo.png" style="width:30.0%" alt="HoloFoodR logo."> <img data-src="https://raw.githubusercontent.com/Bioconductor/BiocStickers/refs/heads/devel/iSEE/iSEE.png" style="width:30.0%" alt="iSEE logo."> <img data-src="https://raw.githubusercontent.com/Bioconductor/BiocStickers/refs/heads/devel/MultiAssayExperiment/MultiAssayExperiment.png" style="width:30.0%" alt="MAE logo."> <img data-src="https://raw.githubusercontent.com/Bioconductor/BiocStickers/refs/heads/devel/SummarizedExperiment/SummarizedExperiment.png" style="width:30.0%" alt="SE logo."> <img data-src="https://raw.githubusercontent.com/Bioconductor/BiocStickers/refs/heads/devel/SingleCellExperiment/SingleCellExperiment.png" style="width:30.0%" alt="SCE logo."> <img data-src="https://raw.githubusercontent.com/Bioconductor/BiocStickers/refs/heads/devel/scater/scater.png" style="width:30.0%" alt="scater logo."> <img data-src="https://pbs.twimg.com/media/FDNU5KgWYAcnU8w.jpg" style="width:30.0%" alt="benchdamic logo."> <img data-src="https://stefpeschel.de/media/logos/NetCoMi_Logo.svg" style="width:30.0%" alt="netcomi logo."></p>
+</div></div>
 </section>
 <section id="advantages" class="slide level2">
 <h2>Advantages</h2>
@@ -653,8 +663,41 @@ <h2>Orchestrating Microbiome Analysis with Bioconductor</h2>
 </section>
 <section id="thank-you-for-your-time" class="slide level2 smaller">
 <h2>Thank you for your time!</h2>
-<p><img data-src="images/paste-DD45BC4A.png" class="quarto-figure quarto-figure-right" width="600"> <small><span style="right"><em>Moreno-Indias et al.&nbsp;(2021)</em></span></small></p>
-<p><img data-src="https://apps.utu.fi/media/logo/UTU_logo_EN_RGB.png" class="quarto-figure quarto-figure-center" alt="University of Turku logo" width="100"> <img data-src="https://www.ebi.ac.uk/metagenomics/static/50d6b60518ea8b4816b9.png" class="quarto-figure quarto-figure-center" alt="UTU logo" width="190"> <img data-src="https://media.aka.fi/api/v3/public/file/497671429c8b0783/thumbnail.jpg?version=e5566c3f8491a9bcc65c74594efa47c0" class="quarto-figure quarto-figure-center" alt="Research Council of Finland logo" width="100"></p>
+<div class="columns">
+<div class="column" style="width:70%;">
+<div class="quarto-figure quarto-figure-center">
+<figure>
+<p><img data-src="images/paste-DD45BC4A.png"></p>
+<figcaption>Moreno-Indias et al.&nbsp;(2021) Statistical and Machine Learning Techniques in Human Microbiome Studies: Contemporary Challenges and Solutions. Frontiers in Microbiology.</figcaption>
+</figure>
+</div>
+</div><div class="column" style="width:30%;">
+<div class="quarto-figure quarto-figure-center">
+<figure>
+<p><img data-src="https://apps.utu.fi/media/logo/UTU_logo_EN_RGB.png" class="quarto-figure quarto-figure-center" alt="University of Turku logo" width="200"></p>
+</figure>
+</div>
+<div class="quarto-figure quarto-figure-center">
+<figure>
+<p><img data-src="https://www.ebi.ac.uk/metagenomics/static/50d6b60518ea8b4816b9.png" class="quarto-figure quarto-figure-center" alt="UTU logo" width="200"></p>
+</figure>
+</div>
+<div class="quarto-figure quarto-figure-center">
+<figure>
+<p><img data-src="https://media.aka.fi/api/v3/public/file/497671429c8b0783/thumbnail.jpg?version=e5566c3f8491a9bcc65c74594efa47c0" class="quarto-figure quarto-figure-center" alt="Research Council of Finland logo" width="200"></p>
+</figure>
+</div>
+<div class="quarto-figure quarto-figure-center">
+<figure>
+<p><img data-src="https://biocityturku.fi/wp-content/uploads/2023/06/CompLifeSci-color-balck-01-2-720x217.png" class="quarto-figure quarto-figure-center" alt="CompLifeSci logo" width="200"></p>
+</figure>
+</div>
+<div class="quarto-figure quarto-figure-center">
+<figure>
+<p><img data-src="https://www.yliopistosaatio.fi/wp-content/uploads/2024/02/logo-vaaka-turun-yliopistosatio.webp" class="quarto-figure quarto-figure-center" alt="Turun yliopistosäätiö logo" width="200"></p>
+</figure>
+</div>
+</div></div>
 
 <div class="quarto-auto-generated-content">
 <p><img src="images/mia_logo.png" class="slide-logo"></p>

diff --git a/docs/oma_files/figure-revealjs/data_and_data_container-1.png b/docs/oma_files/figure-revealjs/data_and_data_container-1.png
diff --git a/docs/oma_files/figure-revealjs/pages_and_book-1.png b/docs/oma_files/figure-revealjs/pages_and_book-1.png
diff --git a/docs/oma_files/figure-revealjs/se_field-1.png b/docs/oma_files/figure-revealjs/se_field-1.png
diff --git a/docs/oma_files/figure-revealjs/show_prevalence-1.png b/docs/oma_files/figure-revealjs/show_prevalence-1.png
diff --git a/docs/quarto.html b/docs/quarto.html
@@ -516,7 +516,7 @@ <h2>Example 2.3: YAML Parameters</h2>
 <p>editor: visual</p>
 <p>smaller: true</p>
 <p>author: Escherichia coli</p>
-<p>date: 2024-11-22</p>
+<p>date: 2024-11-23</p>
 <p><code>---</code></p>
 </section>
 <section id="exercise-2" class="slide level2">

diff --git a/docs/search.json b/docs/search.json
@@ -133,11 +133,11 @@
     "text": "MIcrobiome Analysis (mia)\n\nMicrobiome data science in SummarizedExperiment ecosystem\nDistributed through several R packages\nmia package top 7.6% Bioconductor downloads"
   },
   {
-    "objectID": "oma.html#mia-ecosystem",
-    "href": "oma.html#mia-ecosystem",
+    "objectID": "oma.html#expanding-ecosystem",
+    "href": "oma.html#expanding-ecosystem",
     "title": "Orchestrating Microbiome Analysis with Bioconductor",
-    "section": "mia ecosystem",
-    "text": "mia ecosystem\n\nmia (Data analysis)\nmiaViz (Visualization)\nmiaSim (Simulation)\nmiaTime (Time series analysis)\nmiaDash (Graphical user interface)\niSEEtree (Interactive visualization)\nExpanded by independent developers"
+    "section": "Expanding ecosystem",
+    "text": "Expanding ecosystem\n\n\n\n\nmia (Data analysis)\nmiaViz (Visualization)\nmiaSim (Simulation)\nmiaTime (Time series analysis)\nmiaDash (Graphical user interface)\niSEEtree (Interactive visualization)\nExpanded by independent developers"
   },
   {
     "objectID": "oma.html#advantages",
@@ -214,7 +214,7 @@
     "href": "oma.html#thank-you-for-your-time",
     "title": "Orchestrating Microbiome Analysis with Bioconductor",
     "section": "Thank you for your time!",
-    "text": "Thank you for your time!\n Moreno-Indias et al. (2021)\n  \n\n\n\n\nhttps://microbiome.github.io/"
+    "text": "Thank you for your time!\n\n\n\n\n\nMoreno-Indias et al. (2021) Statistical and Machine Learning Techniques in Human Microbiome Studies: Contemporary Challenges and Solutions. Frontiers in Microbiology.\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\nhttps://microbiome.github.io/"
   },
   {
     "objectID": "hintikkaxo_presentation.html#study-design",
@@ -291,7 +291,7 @@
     "href": "quarto.html#example-2.3-yaml-parameters",
     "title": "Reproducible Reporting with Quarto",
     "section": "Example 2.3: YAML Parameters",
-    "text": "Example 2.3: YAML Parameters\nAt the beginning of any Quarto document, there is a box delimited by ---. There you can define document metadata, such as title, author, date, output format, bibliography, citation style, theme, font size and many others.\n---\ntitle: “Around the gut in 24 hours”\nformat: html\neditor: visual\nsmaller: true\nauthor: Escherichia coli\ndate: 2024-11-22\n---"
+    "text": "Example 2.3: YAML Parameters\nAt the beginning of any Quarto document, there is a box delimited by ---. There you can define document metadata, such as title, author, date, output format, bibliography, citation style, theme, font size and many others.\n---\ntitle: “Around the gut in 24 hours”\nformat: html\neditor: visual\nsmaller: true\nauthor: Escherichia coli\ndate: 2024-11-23\n---"
   },
   {
     "objectID": "quarto.html#exercise-2",

diff --git a/quarto/oma.qmd b/quarto/oma.qmd
@@ -342,19 +342,19 @@ perc <- paste0(round(which(rownames(df) == "mia") / nrow(df), 3)*100, "%")
 ::: columns
 ::: {.column width="70%"}
 
+<!--
 - Community-driven ecosystem of tools
 - Analysis, visualization, simulation, multi-omics, time series, ...
 - Now with a graphical user interface
+-->
 
-<!--
 - [mia](https://bioconductor.org/packages/release/bioc/html/mia.html) (Data analysis)
 - [miaViz](https://bioconductor.org/packages/release/bioc/html/miaViz.html) (Visualization)
 - [miaSim](https://bioconductor.org/packages/release/bioc/html/miaSim.html) (Simulation)
 - [miaTime](https://github.com/microbiome/miaTime) (Time series analysis)
 - [miaDash](https://miadash-microbiome.2.rahtiapp.fi/) (Graphical user interface)
 - [iSEEtree](https://bioconductor.org/packages/release/bioc/html/iSEEtree.html) (Interactive visualization)
 - [Expanded by independent developers](https://microbiome.github.io/OMA/docs/devel/pages/miaverse.html#sec-packages)
--->
 
 :::