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<meta name="author" content="BIOF1001 teaching team" />


<meta name="date" content="2023-11-06" />
<meta name="date" content="2024-08-29" />

<meta name="viewport" content="width=device-width, initial-scale=1" />
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<style type="text/css">
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</ul></li>
<li class="part"><span><b>II Biomedical Data Modules</b></span></li>
<li class="chapter" data-level="5" data-path="image-digital.html"><a href="image-digital.html"><i class="fa fa-check"></i><b>5</b> Medical Image and Digital Health</a></li>
<li class="chapter" data-level="6" data-path="infectious-dis.html"><a href="infectious-dis.html"><i class="fa fa-check"></i><b>6</b> Infectious Disease Informatics</a></li>
<li class="chapter" data-level="7" data-path="cancer.html"><a href="cancer.html"><i class="fa fa-check"></i><b>7</b> Cancer genomics and epidemiology</a>
<li class="chapter" data-level="6" data-path="cancer.html"><a href="cancer.html"><i class="fa fa-check"></i><b>6</b> Cancer genomics and epidemiology</a>
<ul>
<li class="chapter" data-level="7.1" data-path="cancer.html"><a href="cancer.html#cancer-case1"><i class="fa fa-check"></i><b>7.1</b> Case study 1: analysis of cBioportal mutation data</a>
<li class="chapter" data-level="6.1" data-path="cancer.html"><a href="cancer.html#cancer-case1"><i class="fa fa-check"></i><b>6.1</b> Case study 1: analysis of cBioportal mutation data</a>
<ul>
<li class="chapter" data-level="7.1.1" data-path="cancer.html"><a href="cancer.html#exploratory-analysis"><i class="fa fa-check"></i><b>7.1.1</b> Exploratory analysis</a></li>
<li class="chapter" data-level="7.1.2" data-path="cancer.html"><a href="cancer.html#statistical-analysis"><i class="fa fa-check"></i><b>7.1.2</b> Statistical analysis</a></li>
<li class="chapter" data-level="7.1.3" data-path="cancer.html"><a href="cancer.html#literature-search"><i class="fa fa-check"></i><b>7.1.3</b> Literature search</a></li>
<li class="chapter" data-level="6.1.1" data-path="cancer.html"><a href="cancer.html#exploratory-analysis"><i class="fa fa-check"></i><b>6.1.1</b> Exploratory analysis</a></li>
<li class="chapter" data-level="6.1.2" data-path="cancer.html"><a href="cancer.html#statistical-analysis"><i class="fa fa-check"></i><b>6.1.2</b> Statistical analysis</a></li>
<li class="chapter" data-level="6.1.3" data-path="cancer.html"><a href="cancer.html#literature-search"><i class="fa fa-check"></i><b>6.1.3</b> Literature search</a></li>
</ul></li>
<li class="chapter" data-level="7.2" data-path="cancer.html"><a href="cancer.html#cancer-case2"><i class="fa fa-check"></i><b>7.2</b> Case study 2: Cancer Epidemiology</a></li>
<li class="chapter" data-level="7.3" data-path="cancer.html"><a href="cancer.html#scenario"><i class="fa fa-check"></i><b>7.3</b> 1. Scenario</a></li>
<li class="chapter" data-level="7.4" data-path="cancer.html"><a href="cancer.html#hong-kong-population"><i class="fa fa-check"></i><b>7.4</b> 2. Hong Kong population</a>
<li class="chapter" data-level="6.2" data-path="cancer.html"><a href="cancer.html#cancer-case2"><i class="fa fa-check"></i><b>6.2</b> Case study 2: Cancer Epidemiology</a></li>
<li class="chapter" data-level="6.3" data-path="cancer.html"><a href="cancer.html#scenario"><i class="fa fa-check"></i><b>6.3</b> 1. Scenario</a></li>
<li class="chapter" data-level="6.4" data-path="cancer.html"><a href="cancer.html#hong-kong-population"><i class="fa fa-check"></i><b>6.4</b> 2. Hong Kong population</a>
<ul>
<li class="chapter" data-level="7.4.1" data-path="cancer.html"><a href="cancer.html#download-population-data"><i class="fa fa-check"></i><b>7.4.1</b> Download population data</a></li>
<li class="chapter" data-level="7.4.2" data-path="cancer.html"><a href="cancer.html#format-data-for-plotting"><i class="fa fa-check"></i><b>7.4.2</b> Format data for plotting</a></li>
<li class="chapter" data-level="7.4.3" data-path="cancer.html"><a href="cancer.html#plotting-population-data"><i class="fa fa-check"></i><b>7.4.3</b> Plotting population data</a></li>
<li class="chapter" data-level="6.4.1" data-path="cancer.html"><a href="cancer.html#download-population-data"><i class="fa fa-check"></i><b>6.4.1</b> Download population data</a></li>
<li class="chapter" data-level="6.4.2" data-path="cancer.html"><a href="cancer.html#format-data-for-plotting"><i class="fa fa-check"></i><b>6.4.2</b> Format data for plotting</a></li>
<li class="chapter" data-level="6.4.3" data-path="cancer.html"><a href="cancer.html#plotting-population-data"><i class="fa fa-check"></i><b>6.4.3</b> Plotting population data</a></li>
</ul></li>
<li class="chapter" data-level="7.5" data-path="cancer.html"><a href="cancer.html#cancer-registry-data"><i class="fa fa-check"></i><b>7.5</b> 3. Cancer registry data</a>
<li class="chapter" data-level="6.5" data-path="cancer.html"><a href="cancer.html#cancer-registry-data"><i class="fa fa-check"></i><b>6.5</b> 3. Cancer registry data</a>
<ul>
<li class="chapter" data-level="7.5.1" data-path="cancer.html"><a href="cancer.html#download-cancer-registry-data"><i class="fa fa-check"></i><b>7.5.1</b> Download cancer registry data</a></li>
<li class="chapter" data-level="7.5.2" data-path="cancer.html"><a href="cancer.html#a.-visualise-changes-in-incidence-and-mortality"><i class="fa fa-check"></i><b>7.5.2</b> 3a. Visualise changes in incidence and mortality</a></li>
<li class="chapter" data-level="7.5.3" data-path="cancer.html"><a href="cancer.html#b.-calculate-cancer-risk-and-mortality-rate"><i class="fa fa-check"></i><b>7.5.3</b> 3b. Calculate cancer risk and mortality rate</a></li>
<li class="chapter" data-level="7.5.4" data-path="cancer.html"><a href="cancer.html#c.-mortality-incidence-ratio"><i class="fa fa-check"></i><b>7.5.4</b> 3c. Mortality-incidence ratio</a></li>
<li class="chapter" data-level="7.5.5" data-path="cancer.html"><a href="cancer.html#d.-paired-t-test-on-mortality-incidence-ratio-change"><i class="fa fa-check"></i><b>7.5.5</b> 3d. Paired t-test on mortality-incidence ratio change</a></li>
<li class="chapter" data-level="7.5.6" data-path="cancer.html"><a href="cancer.html#e.-childhood-versus-elderly-cancers"><i class="fa fa-check"></i><b>7.5.6</b> 3e. Childhood versus elderly cancers</a></li>
<li class="chapter" data-level="6.5.1" data-path="cancer.html"><a href="cancer.html#download-cancer-registry-data"><i class="fa fa-check"></i><b>6.5.1</b> Download cancer registry data</a></li>
<li class="chapter" data-level="6.5.2" data-path="cancer.html"><a href="cancer.html#a.-visualise-changes-in-incidence-and-mortality"><i class="fa fa-check"></i><b>6.5.2</b> 3a. Visualise changes in incidence and mortality</a></li>
<li class="chapter" data-level="6.5.3" data-path="cancer.html"><a href="cancer.html#b.-calculate-cancer-risk-and-mortality-rate"><i class="fa fa-check"></i><b>6.5.3</b> 3b. Calculate cancer risk and mortality rate</a></li>
<li class="chapter" data-level="6.5.4" data-path="cancer.html"><a href="cancer.html#c.-mortality-incidence-ratio"><i class="fa fa-check"></i><b>6.5.4</b> 3c. Mortality-incidence ratio</a></li>
<li class="chapter" data-level="6.5.5" data-path="cancer.html"><a href="cancer.html#d.-paired-t-test-on-mortality-incidence-ratio-change"><i class="fa fa-check"></i><b>6.5.5</b> 3d. Paired t-test on mortality-incidence ratio change</a></li>
<li class="chapter" data-level="6.5.6" data-path="cancer.html"><a href="cancer.html#e.-childhood-versus-elderly-cancers"><i class="fa fa-check"></i><b>6.5.6</b> 3e. Childhood versus elderly cancers</a></li>
</ul></li>
<li class="chapter" data-level="7.6" data-path="cancer.html"><a href="cancer.html#existing-cancer-funding-and-publication-data"><i class="fa fa-check"></i><b>7.6</b> 4. Existing cancer funding and publication data</a>
<li class="chapter" data-level="6.6" data-path="cancer.html"><a href="cancer.html#existing-cancer-funding-and-publication-data"><i class="fa fa-check"></i><b>6.6</b> 4. Existing cancer funding and publication data</a>
<ul>
<li class="chapter" data-level="7.6.1" data-path="cancer.html"><a href="cancer.html#download-hmrf-grants-and-pubmed-data"><i class="fa fa-check"></i><b>7.6.1</b> Download HMRF grants and Pubmed data</a></li>
<li class="chapter" data-level="7.6.2" data-path="cancer.html"><a href="cancer.html#make-compare-grant-funding-with-incidence-and-mortality"><i class="fa fa-check"></i><b>7.6.2</b> Make compare grant funding with incidence and mortality</a></li>
<li class="chapter" data-level="6.6.1" data-path="cancer.html"><a href="cancer.html#download-hmrf-grants-and-pubmed-data"><i class="fa fa-check"></i><b>6.6.1</b> Download HMRF grants and Pubmed data</a></li>
<li class="chapter" data-level="6.6.2" data-path="cancer.html"><a href="cancer.html#make-word-cloud-for-grants"><i class="fa fa-check"></i><b>6.6.2</b> Make word cloud for grants</a></li>
<li class="chapter" data-level="6.6.3" data-path="cancer.html"><a href="cancer.html#make-compare-grant-funding-with-incidence-and-mortality"><i class="fa fa-check"></i><b>6.6.3</b> Make compare grant funding with incidence and mortality</a></li>
</ul></li>
<li class="chapter" data-level="7.7" data-path="cancer.html"><a href="cancer.html#open-disucssion"><i class="fa fa-check"></i><b>7.7</b> 5. Open disucssion</a></li>
<li class="chapter" data-level="6.7" data-path="cancer.html"><a href="cancer.html#open-disucssion"><i class="fa fa-check"></i><b>6.7</b> 5. Open disucssion</a></li>
</ul></li>
<li class="chapter" data-level="8" data-path="pop-genetics.html"><a href="pop-genetics.html"><i class="fa fa-check"></i><b>8</b> Population Genetics and Diseases</a>
<li class="chapter" data-level="7" data-path="pop-genetics.html"><a href="pop-genetics.html"><i class="fa fa-check"></i><b>7</b> Population Genetics and Diseases</a>
<ul>
<li class="chapter" data-level="8.1" data-path="pop-genetics.html"><a href="pop-genetics.html#case-study-1-heritability-and-human-traits"><i class="fa fa-check"></i><b>8.1</b> Case study 1: Heritability and human traits</a>
<li class="chapter" data-level="7.1" data-path="pop-genetics.html"><a href="pop-genetics.html#case-study-1-heritability-and-human-traits"><i class="fa fa-check"></i><b>7.1</b> Case study 1: Heritability and human traits</a>
<ul>
<li class="chapter" data-level="8.1.1" data-path="pop-genetics.html"><a href="pop-genetics.html#part-1"><i class="fa fa-check"></i><b>8.1.1</b> Part 1</a></li>
<li class="chapter" data-level="8.1.2" data-path="pop-genetics.html"><a href="pop-genetics.html#part-2"><i class="fa fa-check"></i><b>8.1.2</b> Part 2</a></li>
<li class="chapter" data-level="7.1.1" data-path="pop-genetics.html"><a href="pop-genetics.html#part-1"><i class="fa fa-check"></i><b>7.1.1</b> Part 1</a></li>
<li class="chapter" data-level="7.1.2" data-path="pop-genetics.html"><a href="pop-genetics.html#part-2"><i class="fa fa-check"></i><b>7.1.2</b> Part 2</a></li>
<li class="chapter" data-level="7.1.3" data-path="pop-genetics.html"><a href="pop-genetics.html#references"><i class="fa fa-check"></i><b>7.1.3</b> References</a></li>
</ul></li>
</ul></li>
<li class="part"><span><b>III Appendix</b></span></li>
<li class="chapter" data-level="" data-path="install.html"><a href="install.html"><i class="fa fa-check"></i>Appendix A: Install R &amp; RStudio</a>
<ul>
<li class="chapter" data-level="" data-path="install.html"><a href="install.html#a.1-install-r"><i class="fa fa-check"></i>A.1 Install R</a>
<li class="chapter" data-level="" data-path="install.html"><a href="install.html#a.1-install-r-4.3.1"><i class="fa fa-check"></i>A.1 Install R (&gt;=4.3.1)</a>
<ul>
<li class="chapter" data-level="" data-path="install.html"><a href="install.html#r-on-windows"><i class="fa fa-check"></i>R on Windows</a></li>
<li class="chapter" data-level="" data-path="install.html"><a href="install.html#r-on-macos"><i class="fa fa-check"></i>R on macOS</a></li>
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</ul></li>
<li class="chapter" data-level="" data-path="install.html"><a href="install.html#a4.-cloud-computing"><i class="fa fa-check"></i>A4. Cloud computing</a></li>
</ul></li>
<li class="chapter" data-level="" data-path="references.html"><a href="references.html"><i class="fa fa-check"></i>References</a></li>
<li class="chapter" data-level="" data-path="references-1.html"><a href="references-1.html"><i class="fa fa-check"></i>References</a></li>
<li class="divider"></li>
<li><a href="https://github.com/rstudio/bookdown" target="blank">Published with bookdown</a></li>

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<h1><span class="header-section-number">Chapter 5</span> Medical Image and Digital Health<a href="image-digital.html#image-digital" class="anchor-section" aria-label="Anchor link to header"></a></h1>
<!-- # Medical Image and Digital Health {#image-digital} -->
<p>Contents to be added.</p>
<!-- # ```{r child="notebooks/module3-infectious/M3-infectious-dis.Rmd", echo=TRUE} -->
<!-- # ``` -->
<!-- # Personalised Genomic Medicine {#genomics} -->
<!-- ```{r child="notebooks/module1-genomics/M1-genomics-01.Rmd", echo=TRUE} -->
<!-- ``` -->
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