- LyX to write articles and structured documents including citations, Check my blog post on LyX
- JabRef to manage a bibliography
- LaTeX to typeset publications, exported in PDF format
- R statistical software and the R-Studio application
- Several packages: plyr, ggplot2, FAOSTAT, testthat
- Knitr and R Markdown to produce work reports in html. Knitr and LaTeX to produce more elaborate reports in PDF
- xlsx to write data frames to Excel
- I use Firefox (renamed iceweasel on Debian) for web browsing, with the following extensions:
- Adblock to block annoying ads
- Delicious bookmarks to have mobile bookmarks across many browsers
- Mindthetime to keep track of time usage. This extension is not working any more.
- For simple image editing I use Irfanview. I crop scanned pictures or screenshots and I redimension them for web use or use in documents. Very occasionally, I use the "sharpen" function or the brightness, contrast, gamma corrections.
- I use Microsoft word and Excel at work. I use Google documents when writing something at home.
- To work collaboratively I use media wiki with the extension Semantic Mediawiki
- Based in this review, I installed spacesniffer it helps analyse disk space usage on windows. Like Disk space analyser on GNU-Linux systems. You can use filters such as this one: "*.jpg;>100kb;>2weeks" to filter only certain type of files, sizes and dates.
Command line tools on GNU-Linux
- du to analyse disk usage. I created an alias duh for du -h.
- grep to search inside text files
- pdfgrep to search inside pdf documents
- git see programming below
- Writing documents in Lyx
- Keeping track of versions with git
- Managing a bibliography with Jabref.
I want to test
- hubic remote for git annex
- Etherpad (within a company)
- Kaban (within a company)
- Sage mathematics software
- Panda data analysis because it brings data frame structures to python
- Montage Video sur ubuntu and Ubuntu video tools
I stopped using
- QuickWiki Quick search of definitions
- Zotero to share search results with colleagues
- Mendeley to insert citations in Microsoft Word and to manage a bibliography (can import bibtex files form Jabref)
- On this blog, linux users describe their setup
- usethis.com another site where users such as Yihui Xie describe their setup.