Markdown

• JupyText: Jupyter notebooks as Markdown documents
• Generate Google Slides from Markdown
• CriticMarkup - plaintext editing markup for humans

R Markdown

• https://github.com/rstudio/rmarkdown
• R Markdown: The Definitive Guide by Yihui Xie, J. J. Allaire and Garrett Grolemund (2020)
• Authoring books and technical documents with R Markdown by Yihui Xie (2021)
• Create blogs and websites with R Markdown
• Writing reproducible geoscience papers using R Markdown, Docker, and Gitlab by Daniel Nüst, Vicky Steeves, Rémi Rampin, Markus Konkol, Edzer Pebesma (2018)

pandoc

• https://pandoc.org/extras.html
• https://github.com/LaurentRDC/pandoc-plot
• A pandoc-based layout workflow for scholarly journals by Piero (2018)

Quarto

Quarto, by RStudio, sorry, Posit, a new scientific and technical publishing system.

Something to consider, especially if you are new to the field and aren't already invested in the earlier systems.