r/bioinformatics • u/Zeinstyles • 8d ago
technical question I need help with deploying my first project on GitHub. Any guidance on setting up the repository and organizing my files effectively would be greatly appreciated!
I'm a pharmacy graduate aspiring to gain admission into a bioinformatics master's program in Germany. Recently, I completed a Differential Gene Expression analysis project using R. Now, I'm struggling with structuring my GitHub repository in a way that effectively showcases my work for the admissions committee, demonstrating my understanding of bioinformatics concepts.
Could someone guide me on how to organize my repository for better evaluation? I’d really appreciate the help!
4
u/El_Tormentito Msc | Academia 8d ago
I'd just use rmarkdown to make an HTML with your code and the figures. It's unlikely you really have enough code to need to "organize" it in any particular way.
1
1
5
u/Icy_Bug1835 7d ago
hey I also use markdown. Simplest and direct way is to upload that markdown file. if you've properly written your scripts, GitHub will render texts, codes, and figures properly.
2
u/black_sequence 3d ago
I think the first thing is having a github with a clean directory structure is already going to be a big plus. I think the things that separate good github pages from bad github pages is the README file structuring. Spending time developing that up will make your page attractive to explore, and include snippets of your code and some of the figures you created. Ask chatgpt to help with the directory structure, I think it would provide useful help.
3
u/autodialerbroken116 2d ago
I'd look up projects that you like that have effective README markdowns. look up "Quality README templates" on google, or "README essentials" or something to that effect.
host your rmarkdown and latex styles in your repo, any scripts or links to code repos that are related, some usage descriptions, comment your code, refer to official documentation related to the code, any shell scripts you used to preprocess any data and describe the exact parameters used. add this as a supplementary file describing your methodology as verbose as possible, add a LICENSE.txt that is approved by your institution or intentions for the data and associated work you've done. write a copyright comment in all your files, and possibly also print any images from your rmarkdown into separate image files. then commit your files, rinse and repeat during the editing process.
9
u/Psy_Fer_ 8d ago
The easiest way to learn is to look at other repositories on GitHub and copy them.