Connecting to data with R

pure sql actually

http://www.r-bloggers.com/using-sqlite-in-r/

http://faculty.washington.edu/kenrice/sisg-adv/exampleSQLite.R

ORM with dplyr

I use them as references:

http://rpubs.com/justmarkham/dplyr-tutorial
https://www.youtube.com/watch?v=jWjqLW-u3hc&feature=youtu.be

http://rpubs.com/justmarkham/dplyr-tutorial-part-2
https://www.youtube.com/watch?v=2mh1PqfsXVI&feature=youtu.be

package vignettes

https://cran.r-project.org/web/packages/dplyr/vignettes/

Example how to convert MaxQuant output to plyr using R:

http://rpubs.com/witold/115760

Example how to do a join on floats with errors with dplyr, DBI or sqldf

http://rpubs.com/witold/joinonnumeric

Accessing HDF5 with rhdf5

regarding other possibilities see:
http://stackoverflow.com/questions/15974643/how-to-deal-with-hdf5-files-in-r

rhdf5 package vignette
http://www.bioconductor.org/packages//2.13/bioc/vignettes/rhdf5/inst/doc/rhdf5.pdf