I think I leveled up!

As I've previously posted in this community, I am currently a PhD student in bioinformatics, my most usual programing languages are R and Python, and by the way, I decided to start learning C for a better understandid of how things actualy goes under all the abstraction.

It's 2pm now and I'm about 16 hours straight in a new project that passed thru my mind.

It's nothing new, nothing genious, nor even something I couldn't do already. I'll try to be short:

(0) For those who are in here and don't know about gene expression analysis, there is a huge databank called GEO that stores lots and lots of data from RNA/DNA expression of cells, tissues, organs derived from experiments. Already exists plenty of libraries in R and Python that allow us to download and analyse the raw data.

(1) Thus, what is my project and why am I doing something I can already do in minutes? Well, well... I decided to develop a pipeline using the 3 programming languages, to get, arrange, analyse, make plots and a summary/final_report.

(2) What did I do? I used C to act as an orchestrator and to validate the data that I get using R, then Python arrange it, then it goes back to R for analysis and plotting, the it goes back to Python for the report in '.md'

(3) It's still very primitive, but I also am proud of myself, from knowing nothing, to arrange a multi-language-pipeline, all hand-made.

Here is the project tree. I forgot to say that I'm linking the codes using Makefile.

(base) wanderson@wanderson-IdeaPad-1-15IAU7:~/microarray_pipeline$ tree . ├── bin │ └── pipeline ├── build │ ├── filesystem.o │ ├── logger.o │ ├── pipeline.o │ └── process.o ├── data │ ├── metadata │ │ └── sample_info.tsv │ ├── processed │ │ └── clean_metadata.tsv │ └── raw │ └── expression_matrix.tsv ├── docs │ └── NOTES.md ├── Makefile ├── README.md ├── results │ ├── deg │ │ ├── deg_results.tsv │ │ └── deg_significant.tsv │ ├── logs │ │ └── pipeline.log │ ├── plots │ │ ├── heatmap_sig_genes.png │ │ └── volcano_plot.png │ ├── qc │ │ └── pca_plot.png │ └── summary │ ├── analysis_summary.txt │ ├── final_report.html │ └── final_report.md ├── scripts │ ├── python │ │ ├── 01_prepare_metadata.py │ │ ├── 02_check_expression_matrix.py │ │ └── 03_generate_report.py │ ├── r │ │ ├── 02_microarray_limma.R │ │ ├── 03_microarray_pca.R │ │ └── 04_geo_fetch_prepare.R │ └── unix └── src ├── filesystem.c ├── filesystem.h ├── logger.c ├── logger.h ├── pipeline.c ├── process.c └── process.h 19 directories, 33 files