Best software for making figures and diagrams?

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  • ggplot2

    An implementation of the Grammar of Graphics in R

    For data visualization: IMHO nothing beats ggplot2 when it is well used. *Note: Requires knowledge of the R programming language (but there are plenty of resources to learn it and even to cookie cutter recipes for plots. An advantage of knowing R is that protein interactions networks and pathways can also be produced with it (check bioconducotr for resources).

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