Anyway the pandoc markdown that I make can then be turned into:
LaTeX if necessary for academical writing. I use bibtex with jabref currently for managing my bibliography. I use pubmed and google scholar for finding the things. Sci-hub appears good for access problems. Though there's actually even a markdown thesis template converting to LaTeX is v nice to have as a backup.
Word for collaborating on academical writing with people that wont use anything else.
For analytical work I'm lately making use of python in Jupyter Notebook with github and nbviewer and also github gists with Bl.ocks for sharing. With respect to python libraries I Ahave mostly been using pandas, matplotlib, statsmodels and folium.
My editor of choice currently is vim with The Ultimate vimrc.