Last updated: 2019-04-03

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```
Ignored files:
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```
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Expand here to see past versions:

File	Version	Author	Date	Message
Rmd	8d0e8ad	Luke Zappia	2019-04-03	Add Zenodo badge
Rmd	fabb156	Luke Zappia	2019-04-03	Adjust figures and fix names
html	fabb156	Luke Zappia	2019-04-03	Adjust figures and fix names
Rmd	33ac14f	Luke Zappia	2019-03-20	Tidy up website
html	33ac14f	Luke Zappia	2019-03-20	Tidy up website
html	2693e97	Luke Zappia	2019-03-05	Add methods page
Rmd	34eb216	Luke Zappia	2019-02-12	Add velocyto
html	34eb216	Luke Zappia	2019-02-12	Add velocyto
Rmd	8f826ef	Luke Zappia	2019-02-08	Rebuild site and tidy
html	8f826ef	Luke Zappia	2019-02-08	Rebuild site and tidy
Rmd	2daa7f2	Luke Zappia	2019-01-25	Improve output and rebuild
html	2daa7f2	Luke Zappia	2019-01-25	Improve output and rebuild
html	fb2eb66	Luke Zappia	2019-01-10	Tidy workflowr and packrat setup
Rmd	8b1bef9	Luke Zappia	2019-01-10	Start workflowr project.

Expand here to see past versions of organoid-black.png:

Version	Author	Date
33ac14f	Luke Zappia	2019-03-20

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 (Phipson et al. 2019; Combes et al. 2019), focusing on the decisions that are made during analysis and demonstrating a range of tools that can be used for various tasks.

Follow the links below to access the different stages of analysis or refer to the Getting started page for more details about the dataset and how to reproduce the analysis.

Analysis

Pre-processing - Reading of datasets produced using Cell Ranger, comparison of droplet selection methods, annotation of the dataset.
Alevin - Comparison of the alignment-based dataset from Cell Ranger with the same data processed using the alevin method in Salmon.
Quality control - Selection of high-quality cells and removal of uninformative genes.
Clustering - Clustering using the Seurat package with a comparison of methods for gene selection.
Marker genes - Marker gene detection for each cluster using edgeR.
PAGA - Partition-based graph abstraction using the scanpy Python package with visualisation in R.
Cell velocity - Cell velocity estimates using the veloctyo package.

Methods - Description of methods used during the analysis.

Citations

This website and the analysis code can be cited as:

Zappia, Luke. PhD thesis analysis. 2019. DOI: 10.5281/zenodo.2622384

This data files associated with this analysis can be cited as:

Zappia L. PhD thesis analysis data. University of Melbourne. 2019. DOI: 10.26188/5c9182aa7e23d

If you use this data in an analysis please cite the publcations that originally described it.

References

Combes, Alexander N, Luke Zappia, Pei Xuan Er, Alicia Oshlack, and Melissa H Little. 2019. “Single-cell analysis reveals congruence between kidney organoids and human fetal kidney.” Genome Medicine 11 (1): 3. doi:10.1186/s13073-019-0615-0.

Phipson, Belinda, Pei X Er, Alexander N Combes, Thomas A Forbes, Sara E Howden, Luke Zappia, Hsan-Jan Yen, et al. 2019. “Evaluation of variability in human kidney organoids.” Nature Methods 16 (1): 79–87. doi:10.1038/s41592-018-0253-2.

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