R packages for data analyses of pooled CRISPR screens
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