I have been looking for a simple and flexible tool to manage projects, take notes, and track results of data analysis with R, e.g. EverNote, OneNote, Trac, JIRA, github, RMarkdown, bookdown, etc.
Zotero is a free and open-source reference management software to manage bibliographic data and related research materials. Better BibTeX (BBT) is an extension for Zotero and Juris-M that makes it easier to manage bibliographic data.