R packages for data analyses of pooled CRISPR screens We are designing a CRISPR/Cas9 experiment and thinking of the down-stream data analyses. 

Are there any R packages for analysing raw NGS read count data from pooled genetic screens using CRIPSR/Cas9 to disrupt gene expression in a population of cells? I guess we will need to start with basics, i.e. sequences processing, data exploration, visualisation etc.
Assuming you mean CRISPR screens targeting many loci (for example using the GeCKO library) there is an R package here.

It uses a linear mixed effect model to compare guide counts before and after a selection step, allowing for multiple guides/gene and multiple replicates. 
It can also do the initial read alignment AFAIK and the author should be quite responsive in case you have questions.

Another option could be the python program MAGeCK