A tutorial to get started with the computer assisted qualitative data analysis software (CAQDAS) program ATLAS.ti.
Cytoscape is an open source software platform for visualizing complex networks and integrating these with any type of attribute data. Download it here. Cytoscape has apps available for various kinds of problem domains, including bioinformatics, social network analysis, and semantic web.
RStudio develops free and open tools for R and enterprise-ready professional products for teams to scale and share work.