knitr. Reproducible plain-text documents from within R.
Python and SciPy. Python is a general-purpose programming language increasingly used in data manipulation and analysis.
RStudio. An IDE for R. The most straightforward way to get into using R and RMarkdown.
TeX and LaTeX. A typesetting and document preparation system. You can write files in .tex format directly, but it is more useful to just have it available in the background for other tools to use. The MacTeX Distribution is the one to install for macOS.
Pandoc. Converts plain-text documents to and from a wide variety of formats. Can be installed with Homebrew. Be sure to also install pandoc-citeproc for processing citations and bibliographies, and pandoc-crossref for producing cross-references and labels.
Git. Version control system. Installs with Apple’s Developer Tools, or get the latest version via Homebrew.
GNU Make. You tell make what the steps are to create the pieces of a document or program. As you edit and change the various pieces, it automatically figures out which pieces need to be updated and recompiled, and issues the commands to do that. See Karl Broman’s Minimal Make for a short introduction. Make will be installed automatically with Apple’s developer tools.
Zotero, Mendeley, and Papers are citation managers that incorporate PDF storage, annotation and other features. Zotero is free to use. Mendeley has a premium tier. Papers is a paid application after a trial period. I don’t use these tools much, but that’s not for any strong principled reason—mostly just intertia. If you use one and want to integrate with the material here, just make sure it can export to BibTeX/BibLaTeX files. Papers, which I’ve used most recently, can handily output citation keys in pandoc’s format amongst several others.