Another option I'm trying at the moment is the combination of snakemake, conda.io and knitr.

• Conda is a "Package, dependency and environment management for any language" and could be used to set up the R-environment as well as other software. Note, most bioinformatics software can be found in the related bioconda project.

• Snakemake is a workflow management system, which can be used to automate the preprocessing of your data in a reproducible manner (also it works nicely with conda)

• Knitr for dynamic report generation with R. Well suited to document and reproduce your R workflow into reports, ticking your code and seed boxes.

Another option I'm trying at the moment is the combination of snakemake, conda.io and knitr.

• Conda is a "Package, dependency and environment management for any language" and could be used to set up the R-environment as well as other software. Note, most bioinformatics software can be found in the related bioconda project.

• Snakemake is a workflow management system, which can be used to automate the preprocessing of your data in a reproducible manner (also it works nicely with conda since a conda environments can be specified in the Snake-Makefile)

• Knitr for dynamic report generation with R. Well suited to document and reproduce your R workflow into reports, ticking your code and seed boxes.