Introductions

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# Introductions
## & where I'm at

### <span style="color:white;">Gabriel Mateus Bernardo Harrington</span>
### Research Associate<br>Rebecca Sims group
### 2022-05-03 (updated: 2022-04-29)

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# Background

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# Cohort database

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- Series of cohorts Cardiff has been involved in recruiting
- Rich phenotypic data
  - Problem: data not in a structure very amenable to analysis
  - Solution: create relational database to house data in a structure and well controllable manner
    - Used the free and open-source [PostgreSQL](https://www.postgresql.org/)
- General recommendations:
  - Spreadsheets are rubbish
  - Consider using relational databases for anything you actually care about, especially longer term projects and/or ones with lots of people inputting data

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# Whole exsome sequence data

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- Inherited from Didi, she had done a lot of the initial file processing
- Currently grappling with VCF file annotation via [Hail](https://hail.is/)
- Sample IDs also not matching phenotype data very well, see previous point regarding spreadsheets being rubbish
  - Building a lookup table, pending the remaining data coming from the field team
- Data soon&trade; (I hope)

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# Reproducible slides

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- I made a little R package with a template for making slideshows with the DRI theme via RMarkdown/[xaringan](https://github.com/yihui/xaringan)
- Nice ability to easily host slides online, see some of my presentations [here](https://h-mateus.github.io/presentations/)
- Package can be found in this GitHub repo: [H-Mateus/dri.xaringan.theme](https://github.com/H-Mateus/dri.xaringan.theme)
- An example presentation using the DRI (in addition to what you're looking at) can be found [here](https://h-mateus.github.io/presentations/example_dri_theme/index.html#1)
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# Thanks for listening

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<div style="color:skyblue;">
<span style="color:white;"><b>Gabriel Mateus Bernardo Harrington</b></span><br>
<b>Research Assocaite</b><br>
<b></b>
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These slides can be found from the QR code below, or at this address:<br>[https://h-mateus.github.io/presentations/gregynog_2022-04-28/index.html#1](https://h-mateus.github.io/presentations/gregynog_2022-04-28/index.html#1)

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