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Example repository showcasing dynamic and reproducible reporting with R, Quarto, Git, Make, and Docker.

R scripts, transcriptomic data links, and interactive analyses for the Toxoplasma gondii sporulation transcriptome atlas (Hehl Lab, University of Zurich, Vetsuisse Faculty). Includes variance filtering, UMAP/HDBSCAN clustering, differential expression (DEA), over-representation analysis (ORA), stage-specific heatmaps, UpSet and alluvial plots, and interactive network resources.

Code to reproduce results from 'Pawel, S., Heyard, R., Micheloud, C., Held, L. (2023). Replication of null results - Absence of evidence or evidence of absence?'