# My Jupyter notebooks

## Ribosome profiling

* [Multi-frame Ribo-seq and mRNA-seq visualization](ribosome_profiling/ribo_orf_plot.ipynb)

## Gene differential expression

* [Gene differential expression with DESeq2 from Python](deseq_from_python/de.ipynb) and [MA plot](deseq_from_python/de_ma.ipynb). Recommended usage is to download R script [run_deseq.r](deseq_from_python/run_deseq.r) and Python script [de.py](deseq_from_python/de.py), and run the latter on the command line. [de_ma.py](deseq_from_python/de_ma.py) is optional and also usable on the command line. Python scripts are converted to Notebooks using [jupytext](https://github.com/mwouts/jupytext).

## License

*Notebooks* are distributed under the MIT License (see /LICENSE).

Copyright © 2023 Charles E. Vejnar