sfda-carpentries-workshop
Workshop delivered by OSCSA to Saudi FDA
https://github.com/open-science-community-saudi-arabia/sfda-carpentries-workshop
Science Score: 28.0%
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✓CITATION.cff file
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○codemeta.json file
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○.zenodo.json file
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○Academic publication links
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✓Committers with academic emails
12 of 74 committers (16.2%) from academic institutions -
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○Scientific vocabulary similarity
Low similarity (14.6%) to scientific vocabulary
Keywords
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Repository
Workshop delivered by OSCSA to Saudi FDA
Basic Info
- Host: GitHub
- Owner: Open-Science-Community-Saudi-Arabia
- License: other
- Language: Python
- Default Branch: main
- Homepage: https://open-science-community-saudi-arabia.github.io/sFDA-Carpentries-Workshop/
- Size: 147 MB
Statistics
- Stars: 3
- Watchers: 1
- Forks: 8
- Open Issues: 0
- Releases: 0
Topics
Metadata Files
README.md
Intro to R and Open Science Practices for Biologists
This is a workshop delivered by Open Sceince Community Saudi Arabia (OSCSA) for sFDA staff using Carpentries Materials.
Welcome to R!
Working with a programming language (especially if it’s your first time) often feels intimidating, but the rewards outweigh any frustrations. An important secret of coding is that even experienced programmers find it difficult and frustrating at times – so if even the best feel that way, why let intimidation stop you? Given time and practice* you will soon find it easier and easier to accomplish what you want.
Why learn to code?
Bioinformatics – like biology – is messy. Different organisms, different systems, different conditions, all behave differently. Experiments at the bench require a variety of approaches – from tested protocols to trial-and-error. Bioinformatics is also an experimental science, otherwise we could use the same software and same parameters for every genome assembly. Learning to code opens up the full possibilities of computing, especially given that most bioinformatics tools exist only at the command line. Think of it this way: if you could only do molecular biology using a kit, you could probably accomplish a fair amount. However, if you don’t understand the biochemistry of the kit, how would you troubleshoot? How would you do experiments for which there are no kits?
R is one of the most widely-used and powerful programming languages in bioinformatics. R especially shines where a variety of statistical tools are required (e.g. RNA-Seq, population genomics, etc.) and in the generation of publication-quality graphs and figures. Rather than get into an R vs. Python debate (both are useful), keep in mind that many of the concepts you will learn apply to Python and other programming languages.
Finally, we won’t lie; R is not the easiest-to-learn programming language ever created. So, don’t get discouraged! The truth is that even with the modest amount of R we will cover today, you can start using some sophisticated R software packages, and have a general sense of how to interpret an R script. Get through these lessons, and you are on your way to being an accomplished R user!
- We very intentionally used the word practice. One of the other “secrets” of programming is that you can only learn so much by reading about it. Do the exercises in class, re-do them on your own, and then work on your own problems.
Citation and Acknowledgment
How to contribute?
This repository uses GitHub Actions to build and deploy the lesson.
Contributions and Pull Requests should be made against the main branch. After your contribution is merged, Travis will take care of using R to process the Rmd files into markdown files, and push them into the gh-branch which GitHub uses to serve the lesson website.
Participants
- Batool Almarzouq
- Lenah Mukhtar
- Khaloud ALzahrani
- Monah Abou Alezz
- Meshari Alhadlaq
- Amani Alsufyani
- Annajiat Alim Rasel
- Mona Saad Alsharif
- Abdulraman Dallak
- Mashan Aldawsari
- Tala Ahmed Alkharashi
- fahad alreshoodi
- Norah Majed
- Khaloud Alzahrani
- Shatha Alosaimi
- Elaf Alshdokhi
- Noura S. AlMuqati
- Amani T. Alsufyani
- Abdullah A Alajlan
- Ashwaq Alhamed
Individual episode files are in the _episodes_rmd folder.
Owner
- Name: Open Science Community Saudi Arabia
- Login: Open-Science-Community-Saudi-Arabia
- Kind: organization
- Email: admin@openscisaudi.com
- Location: Saudi Arabia
- Website: https://osc-ksa.com/
- Twitter: OpenSciSaudi
- Repositories: 31
- Profile: https://github.com/Open-Science-Community-Saudi-Arabia
Citation (CITATION)
FIXME: describe how to cite this lesson.
GitHub Events
Total
- Watch event: 1
Last Year
- Watch event: 1
Committers
Last synced: 8 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| François Michonneau | f****u@g****m | 132 |
| Greg Wilson | g****n@t****m | 95 |
| Raniere Silva | r****e@r****m | 67 |
| Erin Becker | e****r@g****m | 52 |
| JasonJWilliamsNY | J****Y@g****m | 42 |
| Maxim Belkin | m****n@g****m | 27 |
| Raniere Silva | r****e@i****r | 24 |
| Abigail Cabunoc | a****c@o****a | 24 |
| Ahmed Moustafa | a****a@a****u | 16 |
| Naupaka Zimmerman | n****a@g****m | 14 |
| Katrin Leinweber | 9****r | 13 |
| ytakemon | y****n@g****m | 11 |
| Batool Almarzouq | 5****M | 10 |
| Sarah Stevens | s****2@w****u | 5 |
| Yuka Takemon | y****n | 5 |
| Jason Williams | j****y@g****m | 5 |
| David Mawdsley | d****y@m****k | 4 |
| Piotr Banaszkiewicz | p****r@b****g | 4 |
| Rémi Emonet | r****t@r****e | 4 |
| Janani Ravi | j****i@m****u | 3 |
| Joseph Stachelek | j****a | 3 |
| Zhian N. Kamvar | z****r@g****m | 2 |
| William L. Close | w****e | 2 |
| Michael R. Crusoe | 1****c | 2 |
| Maxim Belkin | m****n | 2 |
| evanwill | e****w@g****m | 2 |
| Raniere Silva | r****7@i****r | 2 |
| LiNk-NY | m****9@g****m | 2 |
| Jon Pipitone | j****e@u****a | 2 |
| James Allen | j****8@g****m | 2 |
| and 44 more... | ||
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 8 months ago
All Time
- Total issues: 0
- Total pull requests: 7
- Average time to close issues: N/A
- Average time to close pull requests: 26 minutes
- Total issue authors: 0
- Total pull request authors: 6
- Average comments per issue: 0
- Average comments per pull request: 0.29
- Merged pull requests: 6
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
Pull Request Authors
- BatoolMM (2)
- kalzahrani1 (1)
- mukhtarl (1)
- Amanitaa89 (1)
- monahton (1)
- meshari323 (1)
Top Labels
Issue Labels
Pull Request Labels
Dependencies
- actions/cache v2 composite
- actions/checkout master composite
- actions/setup-python v2 composite
- r-lib/actions/setup-r v2 composite
- ruby/setup-ruby v1 composite
- actions/cache v2 composite
- actions/checkout master composite
- actions/setup-python v2 composite
- r-lib/actions/setup-r v2 composite
- ruby/setup-ruby v1 composite
- github-pages >= 0 development
- webrick >= 1.6.1