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diff --git a/README.md b/README.md
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 # PhD Thesis Analysis
 
+[![DOI](https://zenodo.org/badge/164960366.svg)](https://zenodo.org/badge/latestdoi/164960366)
+
 This repository contains code and output for the analysis in the analysis
 chapter of my PhD thesis.
 

diff --git a/analysis/index.Rmd b/analysis/index.Rmd
@@ -12,6 +12,8 @@ bibliography:
 knitr::include_graphics("organoid-black.png")
 ```
 
+[![DOI](https://zenodo.org/badge/164960366.svg)](https://zenodo.org/badge/latestdoi/164960366)
+
 This website displays the analysis code and results for the analysis chapter of
 my PhD thesis. In this chapter I reanalyse a previously published kidney
 organoid scRNA-seq dataset [@Phipson2019-er; @Combes2019-uv], focusing on the 
@@ -49,7 +51,7 @@ Citations
 This website and the analysis code can be cited as:
 
 > Zappia, Luke. PhD thesis analysis. 2019.
-> DOI:
+> DOI: [10.5281/zenodo.2622384][zenodo]
 
 This data files associated with this analysis can be cited as:
 
@@ -65,6 +67,7 @@ References
 <div id="refs"></div>
 
 [figshare]: https://melbourne.figshare.com/collections/PhD_thesis_analysis_data/4439804 "Figshare"
+[zenodo]: https://doi.org/10.5281/zenodo.2622384 "Zenodo"
 
 ```{r session-info, eval = FALSE}
 devtools::session_info()

diff --git a/docs/index.html b/docs/index.html
@@ -406,7 +406,7 @@ <h1 class="title toc-ignore">Home</h1>
 </details>
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-<p><details> <summary> <strong style="color:blue;">✔</strong> <strong>Repository version:</strong> <a href="http://github.com/lazappi/phd-thesis-analysis/tree/5870e6e191cf7f91714b40501fc63645582ed59a" target="_blank">5870e6e</a> </summary></p>
+<p><details> <summary> <strong style="color:blue;">✔</strong> <strong>Repository version:</strong> <a href="http://github.com/lazappi/phd-thesis-analysis/tree/8d0e8ad0a8aee623b93113180646e340b1f63761" target="_blank">8d0e8ad</a> </summary></p>
 Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility. The version displayed above was the version of the Git repository at the time these results were generated. <br><br> Note that you need to be careful to ensure that all relevant files for the analysis have been committed to Git prior to generating the results (you can use <code>wflow_publish</code> or <code>wflow_git_commit</code>). workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Below is the status of the Git repository when the results were generated:
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 Ignored files:
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 Untracked files:
     Untracked:  DGEList.Rds
-    Untracked:  output/90-methods/package-versions.json
     Untracked:  scripts/build.pbs
 
-Unstaged changes:
-    Modified:   analysis/_site.yml
-    Modified:   output/01-preprocessing/droplet-selection.pdf
-    Modified:   output/01-preprocessing/parameters.json
-    Modified:   output/01-preprocessing/selection-comparison.pdf
-    Modified:   output/01B-alevin/alevin-comparison.pdf
-    Modified:   output/01B-alevin/parameters.json
-    Modified:   output/02-quality-control/qc-thresholds.pdf
-    Modified:   output/02-quality-control/qc-validation.pdf
-    Modified:   output/03-clustering/cluster-comparison.pdf
-    Modified:   output/03-clustering/cluster-validation.pdf
-    Modified:   output/04-marker-genes/de-results.pdf
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 </code></pre>
 Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes. </details>
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 Rmd
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-<a href="http://github.com/lazappi/phd-thesis-analysis/blob/5870e6e191cf7f91714b40501fc63645582ed59a/analysis/index.Rmd" target="_blank">5870e6e</a>
+<a href="http://github.com/lazappi/phd-thesis-analysis/blob/8d0e8ad0a8aee623b93113180646e340b1f63761/analysis/index.Rmd" target="_blank">8d0e8ad</a>
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+Luke Zappia
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+2019-04-03
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+Add Zenodo badge
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+<a href="http://github.com/lazappi/phd-thesis-analysis/blob/fabb1567c95c26e79732af578909b1f9bbbbb675/analysis/index.Rmd" target="_blank">fabb156</a>
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+Luke Zappia
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+2019-04-03
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+Adjust figures and fix names
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+<a href="https://cdn.rawgit.com/http://github.com/lazappi/phd-thesis-analysis/fabb1567c95c26e79732af578909b1f9bbbbb675/docs/index.html" target="_blank">fabb156</a>
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 Luke Zappia
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+<p><a href="https://zenodo.org/badge/latestdoi/164960366"><img src="https://zenodo.org/badge/164960366.svg" alt="DOI" /></a></p>
 <p>This website displays the analysis code and results for the analysis chapter of my PhD thesis. In this chapter I reanalyse a previously published kidney organoid scRNA-seq dataset <span class="citation">(Phipson et al. 2019; Combes et al. 2019)</span>, focusing on the decisions that are made during analysis and demonstrating a range of tools that can be used for various tasks.</p>
 <p>Follow the links below to access the different stages of analysis or refer to the <a href="getting-started.html">Getting started</a> page for more details about the dataset and how to reproduce the analysis.</p>
 <div id="analysis" class="section level1">
@@ -735,7 +756,7 @@ <h1>Analysis</h1>
 <h1>Citations</h1>
 <p>This website and the analysis code can be cited as:</p>
 <blockquote>
-<p>Zappia, Luke. PhD thesis analysis. 2019. DOI:</p>
+<p>Zappia, Luke. PhD thesis analysis. 2019. DOI: <a href="https://doi.org/10.5281/zenodo.2622384" title="Zenodo">10.5281/zenodo.2622384</a></p>
 </blockquote>
 <p>This data files associated with this analysis can be cited as:</p>
 <blockquote>