SmallSeqFlow: A streamlined, notebook-based bulk RNA-seq analysis pipeline optimized for small-sample studies with modular extensions.

Polynote notebooks for Cross-Species transcriptomics project.

Jupyter notebooks for DGE results and ontology analysis and visualisation.

Python course for omics data analysis covering genomics, transcriptomics, and imagomics. Hands-on Jupyter notebooks for biomedical informatics students.

Dual Python and R notebook that compares ouput for two methods of Gene Set Enrichment Analysis (GSEA) of GSEApy and fGSEA. The webpage version is available at the link below:

The TRN inference and regulon enrichment analysis was done with RTN v. 2.10.1 (Fletcher, Castro et al. 2013) and topGO v. 2.38.1 (Alexa and Rahnenfuhrer 2010). The code is fully available as a R notebook.